diff --git a/DESCRIPTION b/DESCRIPTION index 347eec7..5c59f16 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,6 @@ Imports: dplyr, tidyr, onemap, - GUSMap, ggpubr, plotly, ggplot2, diff --git a/NAMESPACE b/NAMESPACE index 8c1ef5d..468fe85 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -6,11 +6,11 @@ export(efficiency_graphics_mem_cpu) export(efficiency_graphics_perc) export(efficiency_table) export(run_app) -import(GUSMap) import(dplyr) import(ggVennDiagram) import(ggplot2) import(lubridate) +import(mappoly) import(onemap) import(plotly) import(shiny) diff --git a/R/mod_dat_poly.R b/R/mod_dat_poly.R index a450db6..3071e6c 100644 --- a/R/mod_dat_poly.R +++ b/R/mod_dat_poly.R @@ -49,9 +49,7 @@ mod_dat_poly_ui <- function(id){ #' dat_poly Server Functions #' -#' @importFrom ggpubr ggarrange -#' @import onemap -#' @import GUSMap +#' @import mappoly #' @importFrom grDevices dev.off pdf rainbow #' #' @noRd diff --git a/R/mod_emp_maps.R b/R/mod_emp_maps.R index 86ac4a8..476a481 100644 --- a/R/mod_emp_maps.R +++ b/R/mod_emp_maps.R @@ -54,7 +54,6 @@ mod_emp_maps_ui <- function(id){ #' #' @importFrom ggpubr ggarrange #' @import onemap -#' @import GUSMap #' @importFrom grDevices dev.off pdf rainbow #' #' @noRd diff --git a/R/mod_simu_maps.R b/R/mod_simu_maps.R index 71f56bc..5359bcc 100644 --- a/R/mod_simu_maps.R +++ b/R/mod_simu_maps.R @@ -71,7 +71,6 @@ mod_simu_maps_ui <- function(id){ #' simu_maps Server Functions #' #' @import onemap -#' @import GUSMap #' #' @noRd mod_simu_maps_server <- function(input, output, session, datas_simu){ @@ -150,7 +149,7 @@ mod_simu_maps_server <- function(input, output, session, datas_simu){ snpcall = input$SNPCall, countsfrom = input$CountsFrom, data_names = names(datas_simu()[[6]])) data <- datas_simu()[[6]][[temp_n]] - data$rf_2pt() + GUSMap::data$rf_2pt() incProgress(0.5, detail = paste("Doing part", 3)) } else { temp_n <- map_name(depth, seed, geno, fake, @@ -168,7 +167,7 @@ mod_simu_maps_server <- function(input, output, session, datas_simu){ output$map_out <- renderPlot({ if(button1()[[2]] == "gusmap"){ - button1()[[1]]$plotChr(mat="rf", parent = "both") + GUSMap::button1()[[1]]$plotChr(mat="rf", parent = "both") } else { rf_graph_table(button1()[[1]], inter = F, mrk.axis = "none") } diff --git a/inst/ext/toy_sample_emp/biallelics/EmpiricalReads_results.tar.gz b/inst/ext/toy_sample_emp/biallelics/EmpiricalReads_results.tar.gz deleted file mode 100644 index 857cc7b..0000000 Binary files a/inst/ext/toy_sample_emp/biallelics/EmpiricalReads_results.tar.gz and /dev/null differ diff --git a/inst/ext/toy_sample_emp/biallelics/toy_sample_emp.log b/inst/ext/toy_sample_emp/biallelics/toy_sample_emp.log deleted file mode 100644 index 7d8e46e..0000000 --- a/inst/ext/toy_sample_emp/biallelics/toy_sample_emp.log +++ /dev/null @@ -1,8176 +0,0 @@ -[2020-08-08 22:59:50,27] [info] Running with database db.url = jdbc:mysql://127.0.0.1:3307/cromwell?rewriteBatchedStatements=true&useSSL=false -[2020-08-08 22:59:56,20] [info] Running with database db.url = jdbc:mysql://127.0.0.1:3307/cromwell?rewriteBatchedStatements=true&useSSL=false -[INFO] [08/08/2020 22:59:57.025] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor] Workflow heartbeat configuration: -{ - "cromwellId" : "cromid-d100dd9", - "heartbeatInterval" : "2 minutes", - "ttl" : "10 minutes", - "failureShutdownDuration" : "5 minutes", - "writeBatchSize" : 10000, - "writeThreshold" : 10000 -} -[INFO] [08/08/2020 22:59:57.066] [cromwell-system-akka.dispatchers.service-dispatcher-10] [akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/MetadataService] Metadata summary refreshing every 1 second. -[INFO] [08/08/2020 22:59:57.084] [cromwell-system-akka.dispatchers.service-dispatcher-8] [akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/MetadataService/WriteMetadataActor] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. -[INFO] [08/08/2020 22:59:57.084] [cromwell-system-akka.actor.default-dispatcher-4] [akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/KeyValue/KvWriteActor] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. -[INFO] [08/08/2020 22:59:57.095] [cromwell-system-akka.dispatchers.engine-dispatcher-26] [akka://cromwell-system/user/SingleWorkflowRunnerActor/CallCacheWriteActor] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. -[2020-08-08 22:59:57,09] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf) -[INFO] [08/08/2020 22:59:57.148] [cromwell-system-akka.dispatchers.engine-dispatcher-26] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. -[INFO] [08/08/2020 22:59:57.297] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor] SingleWorkflowRunnerActor: Version 49 -[INFO] [08/08/2020 22:59:57.304] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor] SingleWorkflowRunnerActor: Submitting workflow -[INFO] [08/08/2020 22:59:57.344] [cromwell-system-akka.dispatchers.api-dispatcher-32] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreSubmitActor] Unspecified type (Unspecified version) workflow 1408f921-6c91-4dd0-8e32-1871e6da741f submitted -[INFO] [08/08/2020 22:59:57.372] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor] SingleWorkflowRunnerActor: Workflow submitted UUID(1408f921-6c91-4dd0-8e32-1871e6da741f) -[INFO] [08/08/2020 22:59:57.377] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor] 1 new workflows fetched by cromid-d100dd9: 1408f921-6c91-4dd0-8e32-1871e6da741f -[INFO] [08/08/2020 22:59:57.385] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor] WorkflowManagerActor Starting workflow UUID(1408f921-6c91-4dd0-8e32-1871e6da741f) -[INFO] [08/08/2020 22:59:57.392] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor] WorkflowManagerActor Successfully started WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f -[INFO] [08/08/2020 22:59:57.392] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor] Retrieved 1 workflows from the WorkflowStoreActor -[INFO] [08/08/2020 22:59:57.425] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreHeartbeatWriteActor] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. -[INFO] [08/08/2020 22:59:57.506] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(1408f921)]: Parsing workflow as WDL 1.0 -[INFO] [08/08/2020 22:59:59.189] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(1408f921)]: Call-to-Backend assignments: CreateAlignmentFromFamilies.SepareIndividuals -> Local, Maps.vcf2onemap -> Local, GatkGenotyping.BamDepths2Vcf -> Local, FreebayesGenotyping.BamDepths2Vcf -> Local, Maps.Gambis -> Local, SNPCallerMaps.MapsReportEmp -> Local, SNPCallerMaps.FiltersReportEmp -> Local, SupermassaMaps.SupermassaProbs -> Local, SupermassaMaps.FiltersReportEmp -> Local, SNPCallerMaps.CheckDepths -> Local, DefaultMaps.FiltersReportEmp -> Local, CreateAlignmentFromFamilies.RunBwaAlignment -> Local, UpdogMaps.GlobalError -> Local, DefaultMaps.MapsReportEmp -> Local, SupermassaMaps.MapsReportEmp -> Local, FreebayesGenotyping.BamCounts -> Local, UpdogMaps.CheckDepths -> Local, SupermassaMaps.GlobalError -> Local, GusmapMaps.GusmapReport -> Local, SplitFiltVCF.BiallelicNormalization -> Local, GatkGenotyping.HaplotypeCallerERC -> Local, UpdogMaps.UpdogProbs -> Local, Maps.ApplyRandomFilters -> Local, SupermassaMaps.CheckDepths -> Local, SplitFiltVCF.SplitFilters -> Local, PolyradMaps.CheckDepths -> Local, DefaultMaps.GlobalError -> Local, GatkGenotyping.CreateGatkDatabase -> Local, FreebayesGenotyping.FiltChr -> Local, PolyradMaps.MapsReportEmp -> Local, FreebayesGenotyping.RunFreebayes -> Local, SNPCallerMaps.GQProbs -> Local, FreebayesGenotyping.BamCounts4Onemap -> Local, Maps.JointReports -> Local, PolyradMaps.GlobalError -> Local, PolyradMaps.FiltersReportEmp -> Local, DefaultMaps.CheckDepths -> Local, PolyradMaps.PolyradProbs -> Local, GatkGenotyping.GenotypeGVCFs -> Local, GatkGenotyping.BamCounts -> Local, UpdogMaps.MapsReportEmp -> Local, SplitFiltVCF.BiallelicNormalization -> Local, SplitFiltVCF.SplitFilters -> Local, UpdogMaps.FiltersReportEmp -> Local, GatkGenotyping.FiltChr -> Local, GatkGenotyping.BamCounts4Onemap -> Local -[WARN] [08/08/2020 22:59:59.466] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.468] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.468] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.468] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.468] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.469] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.469] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.469] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.469] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.470] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.470] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.470] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.470] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.471] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.471] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.471] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.471] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.472] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.472] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, time, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.472] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.473] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.473] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.474] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.474] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, time, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.474] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.475] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.475] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.475] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.475] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.475] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, time, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.476] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.476] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.476] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.476] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.476] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.477] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.477] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.477] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.477] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.477] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.478] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, time, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.478] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, time, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.478] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [time, mem, cpu] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.478] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[WARN] [08/08/2020 22:59:59.479] [cromwell-system-akka.dispatchers.backend-dispatcher-49] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowInitializationActor-1408f921-6c91-4dd0-8e32-1871e6da741f/Local] Local [UUID(1408f921)]: Key/s [mem, cpu, time] is/are not supported by backend. Unsupported attributes will not be part of job executions. -[INFO] [08/08/2020 23:00:02.162] [cromwell-system-akka.dispatchers.engine-dispatcher-64] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Not triggering log of token queue status. Effective log interval = None -[INFO] [08/08/2020 23:00:05.742] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1] 12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1 [UUID(12088a9f)]: Starting CreateAlignmentFromFamilies.SepareIndividuals -[INFO] [08/08/2020 23:00:06.168] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:00:09,14] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout -[2020-08-08 23:00:09,14] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout -[2020-08-08 23:00:09,15] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc -[2020-08-08 23:00:09,15] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc -[2020-08-08 23:00:09,15] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script -[2020-08-08 23:00:09,15] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script -[2020-08-08 23:00:09,15] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr -[2020-08-08 23:00:09,15] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr -[WARN] [08/08/2020 23:00:09.157] [cromwell-system-akka.dispatchers.engine-dispatcher-17] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.SepareIndividuals:-1:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-SepareIndividuals/execution/rc), invalidating cache entry. -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout -[2020-08-08 23:00:09,37] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -[2020-08-08 23:00:09,37] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -[2020-08-08 23:00:09,38] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc -[2020-08-08 23:00:09,38] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc -[2020-08-08 23:00:09,38] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr -[2020-08-08 23:00:09,38] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr -[2020-08-08 23:00:09,38] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -[2020-08-08 23:00:09,38] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -[WARN] [08/08/2020 23:00:09.384] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.SepareIndividuals:-1:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq), invalidating cache entry. -[2020-08-08 23:00:09,46] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc -[2020-08-08 23:00:09,46] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc -[2020-08-08 23:00:09,46] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -[2020-08-08 23:00:09,46] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -[2020-08-08 23:00:09,46] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script -[2020-08-08 23:00:09,46] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script -[2020-08-08 23:00:09,46] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -[2020-08-08 23:00:09,47] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -[2020-08-08 23:00:09,47] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout -[2020-08-08 23:00:09,47] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout -[2020-08-08 23:00:09,47] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr -[2020-08-08 23:00:09,47] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr -[2020-08-08 23:00:09,47] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -[2020-08-08 23:00:09,47] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -[2020-08-08 23:00:09,47] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -[2020-08-08 23:00:09,48] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -[2020-08-08 23:00:09,48] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -[2020-08-08 23:00:09,48] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -[WARN] [08/08/2020 23:00:09.483] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.SepareIndividuals:-1:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249788.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249786.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249795.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249808.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/data/populus_sub_ig/SRR6249787.sub.fastq -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-SepareIndividuals/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-SepareIndividuals/cacheCopy/execution/script), invalidating cache entry. -[WARN] [08/08/2020 23:00:09.869] [cromwell-system-akka.dispatchers.backend-dispatcher-77] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.SepareIndividuals:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:09.910] [cromwell-system-akka.dispatchers.backend-dispatcher-77] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.SepareIndividuals:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.SepareIndividuals:NA:1]: `python < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai -[2020-08-08 23:00:23,41] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout -[2020-08-08 23:00:23,41] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr -[2020-08-08 23:00:23,41] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc -[2020-08-08 23:00:23,41] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script -[2020-08-08 23:00:23,41] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam -[2020-08-08 23:00:23,41] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam -[WARN] [08/08/2020 23:00:23.419] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:2:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-2/execution/stdout), invalidating cache entry. -[2020-08-08 23:00:23,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -[2020-08-08 23:00:23,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -[2020-08-08 23:00:23,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -[2020-08-08 23:00:23,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -[2020-08-08 23:00:23,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -[2020-08-08 23:00:23,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -[2020-08-08 23:00:23,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -[2020-08-08 23:00:23,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -[2020-08-08 23:00:23,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -[2020-08-08 23:00:23,50] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -[2020-08-08 23:00:23,50] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -[2020-08-08 23:00:23,50] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -[WARN] [08/08/2020 23:00:23.501] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:2:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-2/cacheCopy/execution/script), invalidating cache entry. -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -[2020-08-08 23:00:23,62] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -[2020-08-08 23:00:23,62] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -[WARN] [08/08/2020 23:00:23.632] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:2:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/I_3_66.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-2/cacheCopy/execution/script), invalidating cache entry. -[WARN] [08/08/2020 23:00:23.753] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:23.760] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: `echo /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa.amb /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa.ann /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa.bwt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa.pac /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa.sa -mkdir tmp -export PATH=$PATH:/bin -export PATH=$PATH:/picard.jar - -reads_list=( /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/SRR6249788.sub.fastq ) -lib_list=( I_3_66.Lib1_D06_GCCAACT ) -BAMS=() -for index in ${!reads_list[*]}; do - echo "${reads_list[$index]} is in ${lib_list[$index]}" - bwa_header="@RG\tID:I_3_66.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:I_3_66\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - bwa mem -t 20 -R "${bwa_header}" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/inputs/1874442105/Chr09-10.populus.fa "${reads_list[$index]}" | \ - java -jar /picard.jar SortSam \ - I=/dev/stdin \ - O="I_3_66.${lib_list[$index]}.sorted.bam" \ - TMP_DIR=./tmp \ - SORT_ORDER=coordinate \ - CREATE_INDEX=true; - mv "I_3_66.${lib_list[$index]}.sorted.bai" "I_3_66.${lib_list[$index]}.sorted.bam.bai"; - BAMS+=("I=I_3_66.${lib_list[$index]}.sorted.bam") -done - -if [ "${#BAMS[@]}" -gt 1 ]; then - java -jar /picard.jar MergeSamFiles ${BAMS[@]} \ - O=I_3_66.sorted.bam \ - CREATE_INDEX=true \ - TMP_DIR=./tmp - mv I_3_66.sorted.bai I_3_66.sorted.bam.bai -else - mv I_3_66*.bam I_3_66.sorted.bam - mv I_3_66*.bai I_3_66.sorted.bam.bai -fi` -[INFO] [08/08/2020 23:00:23.768] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2:delegated \ - kfdrc/bwa-picard@sha256:a64d1aaf1268239e70b48e90cb8a75a749fae5966a162112dd901b50c8ef2797 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:00:27.686] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: job id: 29787 -[INFO] [08/08/2020 23:00:27.686] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:00:28.762] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:2:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:00:31.161] [cromwell-system-akka.dispatchers.engine-dispatcher-62] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr -[2020-08-08 23:00:31,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai -[2020-08-08 23:00:31,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai -[WARN] [08/08/2020 23:00:31.497] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:0:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-0/execution/script), invalidating cache entry. -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -[2020-08-08 23:00:31,54] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -[2020-08-08 23:00:31,54] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -[WARN] [08/08/2020 23:00:31.547] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:0:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr), invalidating cache entry. -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -[2020-08-08 23:00:31,59] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -[2020-08-08 23:00:31,59] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -[WARN] [08/08/2020 23:00:31.596] [cromwell-system-akka.dispatchers.engine-dispatcher-22] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:0:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-0/cacheCopy/execution/I_3_56.sorted.bam.bai), invalidating cache entry. -[WARN] [08/08/2020 23:00:31.637] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:31.645] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: `echo /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa.amb /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa.ann /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa.bwt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa.pac /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa.sa -mkdir tmp -export PATH=$PATH:/bin -export PATH=$PATH:/picard.jar - -reads_list=( /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/SRR6249786.sub.fastq ) -lib_list=( I_3_56.Lib1_C10_CCTGCAC ) -BAMS=() -for index in ${!reads_list[*]}; do - echo "${reads_list[$index]} is in ${lib_list[$index]}" - bwa_header="@RG\tID:I_3_56.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:I_3_56\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - bwa mem -t 20 -R "${bwa_header}" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/inputs/1874442105/Chr09-10.populus.fa "${reads_list[$index]}" | \ - java -jar /picard.jar SortSam \ - I=/dev/stdin \ - O="I_3_56.${lib_list[$index]}.sorted.bam" \ - TMP_DIR=./tmp \ - SORT_ORDER=coordinate \ - CREATE_INDEX=true; - mv "I_3_56.${lib_list[$index]}.sorted.bai" "I_3_56.${lib_list[$index]}.sorted.bam.bai"; - BAMS+=("I=I_3_56.${lib_list[$index]}.sorted.bam") -done - -if [ "${#BAMS[@]}" -gt 1 ]; then - java -jar /picard.jar MergeSamFiles ${BAMS[@]} \ - O=I_3_56.sorted.bam \ - CREATE_INDEX=true \ - TMP_DIR=./tmp - mv I_3_56.sorted.bai I_3_56.sorted.bam.bai -else - mv I_3_56*.bam I_3_56.sorted.bam - mv I_3_56*.bai I_3_56.sorted.bam.bai -fi` -[INFO] [08/08/2020 23:00:31.649] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0:delegated \ - kfdrc/bwa-picard@sha256:a64d1aaf1268239e70b48e90cb8a75a749fae5966a162112dd901b50c8ef2797 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:00:32.201] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: job id: 30324 -[INFO] [08/08/2020 23:00:32.202] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:00:36.341] [cromwell-system-akka.dispatchers.backend-dispatcher-85] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:00:40.161] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:00:40,48] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam -[2020-08-08 23:00:40,48] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam -[2020-08-08 23:00:40,48] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout -[2020-08-08 23:00:40,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout -[2020-08-08 23:00:40,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai -[2020-08-08 23:00:40,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai -[2020-08-08 23:00:40,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr -[2020-08-08 23:00:40,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr -[2020-08-08 23:00:40,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script -[2020-08-08 23:00:40,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script -[2020-08-08 23:00:40,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc -[2020-08-08 23:00:40,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc -[WARN] [08/08/2020 23:00:40.494] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:1:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam), invalidating cache entry. -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -[2020-08-08 23:00:40,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -[2020-08-08 23:00:40,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -[WARN] [08/08/2020 23:00:40.536] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:1:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/I_3_55.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-1/cacheCopy/execution/stderr), invalidating cache entry. -[WARN] [08/08/2020 23:00:40.593] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:40.600] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: `echo /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa.amb /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa.ann /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa.bwt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa.pac /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa.sa -mkdir tmp -export PATH=$PATH:/bin -export PATH=$PATH:/picard.jar - -reads_list=( /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/SRR6249787.sub.fastq ) -lib_list=( I_3_55.Lib1_C09_AGAAGTC ) -BAMS=() -for index in ${!reads_list[*]}; do - echo "${reads_list[$index]} is in ${lib_list[$index]}" - bwa_header="@RG\tID:I_3_55.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:I_3_55\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - bwa mem -t 20 -R "${bwa_header}" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/inputs/1874442105/Chr09-10.populus.fa "${reads_list[$index]}" | \ - java -jar /picard.jar SortSam \ - I=/dev/stdin \ - O="I_3_55.${lib_list[$index]}.sorted.bam" \ - TMP_DIR=./tmp \ - SORT_ORDER=coordinate \ - CREATE_INDEX=true; - mv "I_3_55.${lib_list[$index]}.sorted.bai" "I_3_55.${lib_list[$index]}.sorted.bam.bai"; - BAMS+=("I=I_3_55.${lib_list[$index]}.sorted.bam") -done - -if [ "${#BAMS[@]}" -gt 1 ]; then - java -jar /picard.jar MergeSamFiles ${BAMS[@]} \ - O=I_3_55.sorted.bam \ - CREATE_INDEX=true \ - TMP_DIR=./tmp - mv I_3_55.sorted.bai I_3_55.sorted.bam.bai -else - mv I_3_55*.bam I_3_55.sorted.bam - mv I_3_55*.bai I_3_55.sorted.bam.bai -fi` -[INFO] [08/08/2020 23:00:40.604] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1:delegated \ - kfdrc/bwa-picard@sha256:a64d1aaf1268239e70b48e90cb8a75a749fae5966a162112dd901b50c8ef2797 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:00:42.129] [cromwell-system-akka.dispatchers.backend-dispatcher-83] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: job id: 30850 -[INFO] [08/08/2020 23:00:42.130] [cromwell-system-akka.dispatchers.backend-dispatcher-85] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:00:45.131] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:00:49.161] [cromwell-system-akka.dispatchers.engine-dispatcher-26] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:00:49,52] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc -[2020-08-08 23:00:49,52] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc -[2020-08-08 23:00:49,52] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout -[2020-08-08 23:00:49,52] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout -[2020-08-08 23:00:49,52] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script -[2020-08-08 23:00:49,52] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script -[2020-08-08 23:00:49,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,53] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr -[2020-08-08 23:00:49,53] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr -[WARN] [08/08/2020 23:00:49.533] [cromwell-system-akka.dispatchers.engine-dispatcher-17] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:4:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-4/execution/stderr), invalidating cache entry. -[2020-08-08 23:00:49,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,60] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -[2020-08-08 23:00:49,60] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -[2020-08-08 23:00:49,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,61] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -[2020-08-08 23:00:49,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -[2020-08-08 23:00:49,61] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -[2020-08-08 23:00:49,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -[2020-08-08 23:00:49,61] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -[2020-08-08 23:00:49,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -[WARN] [08/08/2020 23:00:49.613] [cromwell-system-akka.dispatchers.engine-dispatcher-56] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:4:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam), invalidating cache entry. -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -[2020-08-08 23:00:49,68] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -[2020-08-08 23:00:49,68] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -[WARN] [08/08/2020 23:00:49.685] [cromwell-system-akka.dispatchers.engine-dispatcher-56] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:4:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/PT_M.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-4/cacheCopy/execution/rc), invalidating cache entry. -[WARN] [08/08/2020 23:00:49.726] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:49.733] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: `echo /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa.amb /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa.ann /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa.bwt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa.pac /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa.sa -mkdir tmp -export PATH=$PATH:/bin -export PATH=$PATH:/picard.jar - -reads_list=( /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/SRR6249808.sub.fastq ) -lib_list=( PT_M.Lib2_E06_CGATGCG ) -BAMS=() -for index in ${!reads_list[*]}; do - echo "${reads_list[$index]} is in ${lib_list[$index]}" - bwa_header="@RG\tID:PT_M.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:PT_M\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - bwa mem -t 20 -R "${bwa_header}" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/inputs/1874442105/Chr09-10.populus.fa "${reads_list[$index]}" | \ - java -jar /picard.jar SortSam \ - I=/dev/stdin \ - O="PT_M.${lib_list[$index]}.sorted.bam" \ - TMP_DIR=./tmp \ - SORT_ORDER=coordinate \ - CREATE_INDEX=true; - mv "PT_M.${lib_list[$index]}.sorted.bai" "PT_M.${lib_list[$index]}.sorted.bam.bai"; - BAMS+=("I=PT_M.${lib_list[$index]}.sorted.bam") -done - -if [ "${#BAMS[@]}" -gt 1 ]; then - java -jar /picard.jar MergeSamFiles ${BAMS[@]} \ - O=PT_M.sorted.bam \ - CREATE_INDEX=true \ - TMP_DIR=./tmp - mv PT_M.sorted.bai PT_M.sorted.bam.bai -else - mv PT_M*.bam PT_M.sorted.bam - mv PT_M*.bai PT_M.sorted.bam.bai -fi` -[INFO] [08/08/2020 23:00:49.737] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4:delegated \ - kfdrc/bwa-picard@sha256:a64d1aaf1268239e70b48e90cb8a75a749fae5966a162112dd901b50c8ef2797 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:00:52.198] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: job id: 31512 -[INFO] [08/08/2020 23:00:52.199] [cromwell-system-akka.dispatchers.backend-dispatcher-91] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:00:53.992] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:4:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:00:55.161] [cromwell-system-akka.dispatchers.engine-dispatcher-56] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr -[2020-08-08 23:00:55,49] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai -[2020-08-08 23:00:55,49] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai -[WARN] [08/08/2020 23:00:55.497] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:3:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/857499da-c7e5-4be1-aacf-273fff65585b/call-SNPCalling/SNPCalling/926e7c07-f5c1-46f8-a9bc-c947d474fc96/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/4245335c-b840-47a8-ad44-5318fc85dacc/call-RunBwaAlignment/shard-3/execution/stderr), invalidating cache entry. -[2020-08-08 23:00:55,55] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -[2020-08-08 23:00:55,55] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -[2020-08-08 23:00:55,55] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -[2020-08-08 23:00:55,55] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -[2020-08-08 23:00:55,55] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,55] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,56] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -[2020-08-08 23:00:55,56] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -[2020-08-08 23:00:55,56] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -[2020-08-08 23:00:55,56] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -[2020-08-08 23:00:55,56] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -[2020-08-08 23:00:55,56] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -[WARN] [08/08/2020 23:00:55.563] [cromwell-system-akka.dispatchers.engine-dispatcher-17] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:3:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/2b58608c-6afb-4e9e-9b76-2280d7769ccc/call-SNPCalling/SNPCalling/5e969616-1621-4e5d-a88b-a7d25850cb35/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/fbb61ba6-8a95-4d4d-b5b2-af4d81f0dbce/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout), invalidating cache entry. -[2020-08-08 23:00:55,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -[2020-08-08 23:00:55,60] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -[2020-08-08 23:00:55,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,60] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -[2020-08-08 23:00:55,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -[2020-08-08 23:00:55,60] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -[2020-08-08 23:00:55,60] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -[2020-08-08 23:00:55,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -[2020-08-08 23:00:55,61] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -[2020-08-08 23:00:55,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -[2020-08-08 23:00:55,61] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -[2020-08-08 23:00:55,61] [warn] Localization via copy has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -[WARN] [08/08/2020 23:00:55.612] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1] 12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1 [UUID(12088a9f)]: Failed copying cache results for job BackendJobDescriptorKey_CommandCallNode_CreateAlignmentFromFamilies.RunBwaAlignment:3:1 (AggregatedException: : -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stdout -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/rc -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/PT_F.sorted.bam.bai -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/stderr -Could not cache /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script: - /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script doesn't exist - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script - File not found /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/707e72fe-e6b0-4302-a02b-23781202e554/call-SNPCalling/SNPCalling/cbc25168-6ad3-4de5-a2e6-84f8eb9f9572/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/ce8418a9-7f75-4858-ab30-41f0201f0ef5/call-RunBwaAlignment/shard-3/cacheCopy/execution/script), invalidating cache entry. -[WARN] [08/08/2020 23:00:55.652] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:00:55.658] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: `echo /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa.amb /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa.ann /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa.bwt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa.pac /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa.sa -mkdir tmp -export PATH=$PATH:/bin -export PATH=$PATH:/picard.jar - -reads_list=( /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/SRR6249795.sub.fastq ) -lib_list=( PT_F.Lib1_E09_TGAACAT ) -BAMS=() -for index in ${!reads_list[*]}; do - echo "${reads_list[$index]} is in ${lib_list[$index]}" - bwa_header="@RG\tID:PT_F.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:PT_F\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - bwa mem -t 20 -R "${bwa_header}" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/inputs/1874442105/Chr09-10.populus.fa "${reads_list[$index]}" | \ - java -jar /picard.jar SortSam \ - I=/dev/stdin \ - O="PT_F.${lib_list[$index]}.sorted.bam" \ - TMP_DIR=./tmp \ - SORT_ORDER=coordinate \ - CREATE_INDEX=true; - mv "PT_F.${lib_list[$index]}.sorted.bai" "PT_F.${lib_list[$index]}.sorted.bam.bai"; - BAMS+=("I=PT_F.${lib_list[$index]}.sorted.bam") -done - -if [ "${#BAMS[@]}" -gt 1 ]; then - java -jar /picard.jar MergeSamFiles ${BAMS[@]} \ - O=PT_F.sorted.bam \ - CREATE_INDEX=true \ - TMP_DIR=./tmp - mv PT_F.sorted.bai PT_F.sorted.bam.bai -else - mv PT_F*.bam PT_F.sorted.bam - mv PT_F*.bai PT_F.sorted.bam.bai -fi` -[INFO] [08/08/2020 23:00:55.662] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3:delegated \ - kfdrc/bwa-picard@sha256:a64d1aaf1268239e70b48e90cb8a75a749fae5966a162112dd901b50c8ef2797 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:00:57.135] [cromwell-system-akka.dispatchers.backend-dispatcher-86] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: job id: 31943 -[INFO] [08/08/2020 23:00:57.136] [cromwell-system-akka.dispatchers.backend-dispatcher-91] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:01:01.631] [cromwell-system-akka.dispatchers.backend-dispatcher-84] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-EngineJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/12088a9f-28b2-40a2-b329-964946cf15a5-BackendJobExecutionActor-CreateAlignmentFromFamilies.RunBwaAlignment:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(12088a9f)CreateAlignmentFromFamilies.RunBwaAlignment:3:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:01:05.949] [cromwell-system-akka.dispatchers.engine-dispatcher-61] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1/12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1] 12088a9f-28b2-40a2-b329-964946cf15a5-SubWorkflowActor-SubWorkflow-CreateAlignmentFromFamilies:-1:1 [UUID(12088a9f)]: Workflow CreateAlignmentFromFamilies complete. Final Outputs: -{ - "CreateAlignmentFromFamilies.bam": "[\"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam\", \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam\", \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam...", - "CreateAlignmentFromFamilies.bai": "[\"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai\", \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai\", \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.so...", - "CreateAlignmentFromFamilies.names": ["I_3_56", "I_3_55", "I_3_66", "PT_F", "PT_M"], - "CreateAlignmentFromFamilies.alignments": "[typed object {bam: \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam\", bai: \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai\", sample: \"I_3_56\"}, typed object {bam: \"/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964..." -} -[INFO] [08/08/2020 23:01:09.942] [cromwell-system-akka.dispatchers.engine-dispatcher-64] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Starting FreebayesGenotyping.RunFreebayes -[INFO] [08/08/2020 23:01:10.162] [cromwell-system-akka.dispatchers.engine-dispatcher-19] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[INFO] [08/08/2020 23:01:12.001] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.HaplotypeCallerERC (5 shards) -[WARN] [08/08/2020 23:01:12.010] [cromwell-system-akka.dispatchers.backend-dispatcher-93] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:01:12,01] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/575655112/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam: Operation not permitted -[2020-08-08 23:01:12,01] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-1221296247/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1276719690/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-520231669/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1977784268/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/575655112/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-1221296247/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1276719690/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-520231669/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai: Operation not permitted -[2020-08-08 23:01:12,02] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1977784268/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai: Operation not permitted -[INFO] [08/08/2020 23:01:12.031] [cromwell-system-akka.dispatchers.backend-dispatcher-93] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: `freebayes-parallel <(fasta_generate_regions.py /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1874442105/Chr09-10.populus.fa.fai 100000) 20 \ ---genotype-qualities -f /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1874442105/Chr09-10.populus.fa /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/575655112/I_3_56.sorted.bam /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-1221296247/I_3_55.sorted.bam /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1276719690/I_3_66.sorted.bam /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/-520231669/PT_F.sorted.bam /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/inputs/1977784268/PT_M.sorted.bam > "freebayes.vcf"` -[INFO] [08/08/2020 23:01:12.034] [cromwell-system-akka.dispatchers.backend-dispatcher-93] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes:delegated \ - taniguti/freebayes@sha256:dafd8e404f816c2f7648065753618e4b057ddffa811b42bd4723b03d55db2b60 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:01:12.270] [cromwell-system-akka.dispatchers.backend-dispatcher-92] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: job id: 409 -[INFO] [08/08/2020 23:01:12.271] [cromwell-system-akka.dispatchers.backend-dispatcher-94] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:01:47.351] [cromwell-system-akka.dispatchers.backend-dispatcher-96] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.RunFreebayes:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.RunFreebayes:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:01:49.161] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:01:50.910] [cromwell-system-akka.dispatchers.backend-dispatcher-97] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:01:50,91] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/inputs/1276719690/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai: Operation not permitted -[2020-08-08 23:01:50,91] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/inputs/1276719690/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:01:50.918] [cromwell-system-akka.dispatchers.backend-dispatcher-97] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: `/gatk/gatk HaplotypeCaller \ - -ERC GVCF \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/inputs/1874442105/Chr09-10.populus.fa \ - -I /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/inputs/1276719690/I_3_66.sorted.bam \ - -O I_3_66_rawLikelihoods.g.vcf \ - --max-reads-per-alignment-start 0` -[INFO] [08/08/2020 23:01:50.921] [cromwell-system-akka.dispatchers.backend-dispatcher-97] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:01:51.552] [cromwell-system-akka.dispatchers.engine-dispatcher-61] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(7fafa422)]: Starting SplitFiltVCF.BiallelicNormalization -[INFO] [08/08/2020 23:01:52.263] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: job id: 2559 -[INFO] [08/08/2020 23:01:52.264] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:02:42.991] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:2:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:02:46.161] [cromwell-system-akka.dispatchers.engine-dispatcher-61] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:02:46.292] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:02:46,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/inputs/1977784268/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai: Operation not permitted -[2020-08-08 23:02:46,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/inputs/1977784268/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:02:46.298] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: `/gatk/gatk HaplotypeCaller \ - -ERC GVCF \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/inputs/1874442105/Chr09-10.populus.fa \ - -I /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/inputs/1977784268/PT_M.sorted.bam \ - -O PT_M_rawLikelihoods.g.vcf \ - --max-reads-per-alignment-start 0` -[INFO] [08/08/2020 23:02:46.300] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:02:47.209] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: job id: 4966 -[INFO] [08/08/2020 23:02:47.209] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:03:36.761] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:4:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:03:40.161] [cromwell-system-akka.dispatchers.engine-dispatcher-65] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:03:40.283] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:03:40,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/inputs/575655112/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai: Operation not permitted -[2020-08-08 23:03:40,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/inputs/575655112/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:03:40.289] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: `/gatk/gatk HaplotypeCaller \ - -ERC GVCF \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/inputs/1874442105/Chr09-10.populus.fa \ - -I /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/inputs/575655112/I_3_56.sorted.bam \ - -O I_3_56_rawLikelihoods.g.vcf \ - --max-reads-per-alignment-start 0` -[INFO] [08/08/2020 23:03:40.293] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:03:42.214] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: job id: 7367 -[INFO] [08/08/2020 23:03:42.215] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:04:25.181] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:04:28.161] [cromwell-system-akka.dispatchers.engine-dispatcher-22] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:04:28.283] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:04:28,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/inputs/-1221296247/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai: Operation not permitted -[2020-08-08 23:04:28,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/inputs/-1221296247/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:04:28.289] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: `/gatk/gatk HaplotypeCaller \ - -ERC GVCF \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/inputs/1874442105/Chr09-10.populus.fa \ - -I /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/inputs/-1221296247/I_3_55.sorted.bam \ - -O I_3_55_rawLikelihoods.g.vcf \ - --max-reads-per-alignment-start 0` -[INFO] [08/08/2020 23:04:28.292] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:04:32.137] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: job id: 9379 -[INFO] [08/08/2020 23:04:32.137] [cromwell-system-akka.dispatchers.backend-dispatcher-99] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:05:14.791] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:05:16.161] [cromwell-system-akka.dispatchers.engine-dispatcher-23] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:05:16.282] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:05:16,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/inputs/-520231669/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai: Operation not permitted -[2020-08-08 23:05:16,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/inputs/-520231669/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:05:16.287] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: `/gatk/gatk HaplotypeCaller \ - -ERC GVCF \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/inputs/1874442105/Chr09-10.populus.fa \ - -I /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/inputs/-520231669/PT_F.sorted.bam \ - -O PT_F_rawLikelihoods.g.vcf \ - --max-reads-per-alignment-start 0` -[INFO] [08/08/2020 23:05:16.290] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:05:17.180] [cromwell-system-akka.dispatchers.backend-dispatcher-98] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: job id: 11526 -[INFO] [08/08/2020 23:05:17.180] [cromwell-system-akka.dispatchers.backend-dispatcher-102] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:06:06.721] [cromwell-system-akka.dispatchers.backend-dispatcher-97] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.HaplotypeCallerERC:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.HaplotypeCallerERC:3:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:06:10.161] [cromwell-system-akka.dispatchers.engine-dispatcher-57] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[INFO] [08/08/2020 23:06:11.352] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.CreateGatkDatabase -[WARN] [08/08/2020 23:06:11.965] [cromwell-system-akka.dispatchers.backend-dispatcher-105] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:06:11,96] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/inputs/-236587406/freebayes.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-RunFreebayes/execution/freebayes.vcf: Operation not permitted -[INFO] [08/08/2020 23:06:11.971] [cromwell-system-akka.dispatchers.backend-dispatcher-105] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: `bcftools norm /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/inputs/-236587406/freebayes.vcf --rm-dup all -Ov --check-ref w -f /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/inputs/1874442105/Chr09-10.populus.fa > vcf_norm.vcf` -[INFO] [08/08/2020 23:06:11.973] [cromwell-system-akka.dispatchers.backend-dispatcher-105] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization:delegated \ - lifebitai/bcftools@sha256:72035b7978657b3acd314052ce78f4bd9dac0eca885e1797fbb06603ad3bd404 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:06:12.579] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: job id: 14101 -[INFO] [08/08/2020 23:06:12.579] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:06:16.821] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.BiallelicNormalization:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:06:19.161] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/110509716/I_3_56_rawLikelihoods.g.vcf.idx -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/I_3_56_rawLikelihoods.g.vcf.idx: Operation not permitted -[WARN] [08/08/2020 23:06:19.318] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-1686441643/I_3_55_rawLikelihoods.g.vcf.idx -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/I_3_55_rawLikelihoods.g.vcf.idx: Operation not permitted -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/811574294/I_3_66_rawLikelihoods.g.vcf.idx -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/I_3_66_rawLikelihoods.g.vcf.idx: Operation not permitted -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-985377065/PT_F_rawLikelihoods.g.vcf.idx -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/PT_F_rawLikelihoods.g.vcf.idx: Operation not permitted -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/1512638872/PT_M_rawLikelihoods.g.vcf.idx -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/PT_M_rawLikelihoods.g.vcf.idx: Operation not permitted -[2020-08-08 23:06:19,32] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/110509716/I_3_56_rawLikelihoods.g.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-0/execution/I_3_56_rawLikelihoods.g.vcf: Operation not permitted -[2020-08-08 23:06:19,33] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-1686441643/I_3_55_rawLikelihoods.g.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-1/execution/I_3_55_rawLikelihoods.g.vcf: Operation not permitted -[2020-08-08 23:06:19,33] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/811574294/I_3_66_rawLikelihoods.g.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-2/execution/I_3_66_rawLikelihoods.g.vcf: Operation not permitted -[2020-08-08 23:06:19,33] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-985377065/PT_F_rawLikelihoods.g.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-3/execution/PT_F_rawLikelihoods.g.vcf: Operation not permitted -[2020-08-08 23:06:19,33] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/1512638872/PT_M_rawLikelihoods.g.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-HaplotypeCallerERC/shard-4/execution/PT_M_rawLikelihoods.g.vcf: Operation not permitted -[INFO] [08/08/2020 23:06:19.341] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: `grep ">" /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/1874442105/Chr09-10.populus.fa > interval_list_temp -sed 's/^.//' interval_list_temp > interval.list - -/gatk/gatk GenomicsDBImport \ - --genomicsdb-workspace-path my_database \ - -L interval.list \ - -V /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/110509716/I_3_56_rawLikelihoods.g.vcf -V /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-1686441643/I_3_55_rawLikelihoods.g.vcf -V /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/811574294/I_3_66_rawLikelihoods.g.vcf -V /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/-985377065/PT_F_rawLikelihoods.g.vcf -V /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/inputs/1512638872/PT_M_rawLikelihoods.g.vcf - -tar -cf my_database.tar my_database` -[INFO] [08/08/2020 23:06:19.344] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:06:19.591] [cromwell-system-akka.dispatchers.engine-dispatcher-22] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(7fafa422)]: Starting SplitFiltVCF.SplitFilters -[INFO] [08/08/2020 23:06:22.196] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: job id: 14620 -[INFO] [08/08/2020 23:06:22.197] [cromwell-system-akka.dispatchers.backend-dispatcher-106] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:06:38.501] [cromwell-system-akka.dispatchers.backend-dispatcher-107] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.CreateGatkDatabase:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.CreateGatkDatabase:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:06:40.161] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[INFO] [08/08/2020 23:06:40.922] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.GenotypeGVCFs -[WARN] [08/08/2020 23:06:41.147] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:06:41,14] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/inputs/1714835832/vcf_norm.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-BiallelicNormalization/execution/vcf_norm.vcf: Operation not permitted -[INFO] [08/08/2020 23:06:41.157] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: `vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/inputs/1714835832/vcf_norm.vcf --min-alleles 3 --recode --out freebayes_multi1 - -vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/inputs/1714835832/vcf_norm.vcf --min-alleles 2 --max-alleles 2 --recode --out freebayes_bi1 - -Rscript /opt/scripts/split.R freebayes_bi1.recode.vcf PT_F PT_M position_multi2.txt - -vcftools --vcf freebayes_bi1.recode.vcf --positions position_multi2.txt --recode --out freebayes_multi2 - -vcftools --vcf freebayes_bi1.recode.vcf --exclude-positions position_multi2.txt --recode --out freebayes_bi - -vcf-concat freebayes_multi1.recode.vcf freebayes_multi2.recode.vcf > freebayes_multi.recode.vcf - -vcftools --gzvcf freebayes_multi.recode.vcf --chr Chr10 --recode --out freebayes_multi_Chr10 - -vcftools --vcf freebayes_bi.recode.vcf --chr Chr10 --recode --out freebayes_bi_Chr10 - -bgzip freebayes_multi.recode.vcf -bgzip freebayes_bi_Chr10.recode.vcf -tabix -p vcf freebayes_bi_Chr10.recode.vcf.gz -bgzip freebayes_multi_Chr10.recode.vcf -bgzip freebayes_bi.recode.vcf` -[INFO] [08/08/2020 23:06:41.159] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters:delegated \ - cristaniguti/vcftools@sha256:8510a07715463f02d5cbc57a92aae51b9c6b83bfacf922f61b433e3757644b76 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:06:42.490] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: job id: 15499 -[INFO] [08/08/2020 23:06:42.491] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:06:47.751] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7fafa422)SplitFiltVCF.SplitFilters:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:06:49.161] [cromwell-system-akka.dispatchers.engine-dispatcher-62] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:06:49.282] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:06:49,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/inputs/-523154733/my_database.tar -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-CreateGatkDatabase/execution/my_database.tar: Operation not permitted -[INFO] [08/08/2020 23:06:49.286] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: `tar -xf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/inputs/-523154733/my_database.tar -WORKSPACE=$( basename /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/inputs/-523154733/my_database.tar .tar) - -/gatk/gatk GenotypeGVCFs \ - -R /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/inputs/1874442105/Chr09-10.populus.fa \ - -O gatk.vcf.gz \ - -G StandardAnnotation \ - -V gendb://$WORKSPACE` -[INFO] [08/08/2020 23:06:49.288] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:06:50.192] [cromwell-system-akka.dispatchers.engine-dispatcher-26] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 7fafa422-034b-4c9a-9d9f-3dbb290e22d7-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(7fafa422)]: Workflow SplitFiltVCF complete. Final Outputs: -{ - "SplitFiltVCF.vcf_bi_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi.recode.vcf.gz", - "SplitFiltVCF.vcf_bi_chr_norm_tbi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi", - "SplitFiltVCF.vcf_bi_chr_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz", - "SplitFiltVCF.vcf_multi_chr": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi_Chr10.recode.vcf.gz", - "SplitFiltVCF.vcf_multi_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi.recode.vcf.gz" -} -[INFO] [08/08/2020 23:06:52.141] [cromwell-system-akka.dispatchers.engine-dispatcher-61] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Starting FreebayesGenotyping.BamCounts (5 shards) -[INFO] [08/08/2020 23:06:52.301] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: job id: 15995 -[INFO] [08/08/2020 23:06:52.303] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:07:00.771] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.GenotypeGVCFs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.GenotypeGVCFs:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:07:04.161] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:07:04.286] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:07:04,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:07:04,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:07:04,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai: Operation not permitted -[2020-08-08 23:07:04,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:07:04.293] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_56_freebayes_counts.tsv"` -[INFO] [08/08/2020 23:07:04.295] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:07:06.421] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(1880a9f4)]: Starting SplitFiltVCF.BiallelicNormalization -[INFO] [08/08/2020 23:07:07.139] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: job id: 16722 -[INFO] [08/08/2020 23:07:07.140] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:07:12.441] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:07:15.161] [cromwell-system-akka.dispatchers.engine-dispatcher-57] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:07:15.280] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:07:15,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:07:15,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:07:15,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai: Operation not permitted -[2020-08-08 23:07:15,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:07:15.286] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_55_freebayes_counts.tsv"` -[INFO] [08/08/2020 23:07:15.289] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:07:17.330] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: job id: 17402 -[INFO] [08/08/2020 23:07:17.330] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:07:24.062] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:07:25.161] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:07:25.285] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:07:25,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:07:25,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:07:25,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai: Operation not permitted -[2020-08-08 23:07:25,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:07:25.292] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_66_freebayes_counts.tsv"` -[INFO] [08/08/2020 23:07:25.294] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:07:27.243] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: job id: 18032 -[INFO] [08/08/2020 23:07:27.243] [cromwell-system-akka.dispatchers.backend-dispatcher-110] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:07:36.331] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:2:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:07:40.161] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:07:40.305] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:07:40,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:07:40,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:07:40,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai: Operation not permitted -[2020-08-08 23:07:40,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:07:40.312] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "PT_M_freebayes_counts.tsv"` -[INFO] [08/08/2020 23:07:40.314] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:07:42.135] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: job id: 18878 -[INFO] [08/08/2020 23:07:42.135] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:07:48.591] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:4:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:07:52.161] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:07:52.287] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:07:52,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:07:52,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:07:52,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai: Operation not permitted -[2020-08-08 23:07:52,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:07:52.297] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "PT_F_freebayes_counts.tsv"` -[INFO] [08/08/2020 23:07:52.299] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:07:57.171] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: job id: 19568 -[INFO] [08/08/2020 23:07:57.171] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:01.831] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts:3:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:04.161] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:08:04.273] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:04,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/inputs/1436039663/gatk.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-GenotypeGVCFs/execution/gatk.vcf.gz: Operation not permitted -[INFO] [08/08/2020 23:08:04.291] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: `bcftools norm /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/inputs/1436039663/gatk.vcf.gz --rm-dup all -Ov --check-ref w -f /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/inputs/1874442105/Chr09-10.populus.fa > vcf_norm.vcf` -[INFO] [08/08/2020 23:08:04.293] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization:delegated \ - lifebitai/bcftools@sha256:72035b7978657b3acd314052ce78f4bd9dac0eca885e1797fbb06603ad3bd404 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:05.552] [cromwell-system-akka.dispatchers.engine-dispatcher-24] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Starting FreebayesGenotyping.BamCounts4Onemap -[INFO] [08/08/2020 23:08:07.190] [cromwell-system-akka.dispatchers.backend-dispatcher-108] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: job id: 20237 -[INFO] [08/08/2020 23:08:07.191] [cromwell-system-akka.dispatchers.backend-dispatcher-111] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:08.691] [cromwell-system-akka.dispatchers.backend-dispatcher-109] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.BiallelicNormalization:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.BiallelicNormalization:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:10.161] [cromwell-system-akka.dispatchers.engine-dispatcher-56] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[INFO] [08/08/2020 23:08:10.671] [cromwell-system-akka.dispatchers.engine-dispatcher-56] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(1880a9f4)]: Starting SplitFiltVCF.SplitFilters -[WARN] [08/08/2020 23:08:11.809] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:11,81] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/inputs/-176373035/I_3_56_freebayes_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-0/execution/I_3_56_freebayes_counts.tsv: Operation not permitted -[2020-08-08 23:08:11,81] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/inputs/-1973324394/I_3_55_freebayes_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-1/execution/I_3_55_freebayes_counts.tsv: Operation not permitted -[2020-08-08 23:08:11,81] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/inputs/524691543/I_3_66_freebayes_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-2/execution/I_3_66_freebayes_counts.tsv: Operation not permitted -[2020-08-08 23:08:11,81] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/inputs/-1272259816/PT_F_freebayes_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-3/execution/PT_F_freebayes_counts.tsv: Operation not permitted -[2020-08-08 23:08:11,81] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/inputs/1225756121/PT_M_freebayes_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts/shard-4/execution/PT_M_freebayes_counts.tsv: Operation not permitted -[INFO] [08/08/2020 23:08:11.819] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: `R --vanilla --no-save < idx")) - idx <- read.table("idx", stringsAsFactors = F) - idx <- strsplit(idx[,1], ":")[[1]][1] - idx <- as.numeric(idx) -1 - - file.counts <- read.table(paste0(names[1],"_", "freebayes","_counts.tsv"), skip = idx, header=T, stringsAsFactors = F) - - ref_depth_matrix2 <- alt_depth_matrix2 <- matrix(NA, nrow = dim(file.counts)[1], ncol = length(names)) - - for(j in 1:length(names)){ - ## From picard tool - - file.counts <- read.table(paste0(names[j],"_", "freebayes","_counts.tsv"), skip = idx, header=T, stringsAsFactors = F) - - ref_depth_matrix2[,j] <- file.counts[,3] - alt_depth_matrix2[,j] <- file.counts[,4] - - if(j == 1){ - ref_allele <- file.counts[,5] - alt_allele <- file.counts[,6] - } else { - idx.ref <- which(ref_allele == "N") - idx.alt <- which(alt_allele == "N") - if(length(idx.ref)!=0){ - ref_allele[idx.ref] <- file.counts[idx.ref,5] - } - if(length(idx.alt)!=0){ - alt_allele[idx.alt] <- file.counts[idx.alt,6] - } - } - } - - rownames(ref_depth_matrix2) <- rownames(alt_depth_matrix2) <- paste0(file.counts[,1],"_", file.counts[,2]) - colnames(ref_depth_matrix2) <- colnames(alt_depth_matrix2) <- names - - alleles <- data.frame(file.counts[,1],file.counts[,2], ref_allele, alt_allele) - write.table(alleles, file = paste0("freebayes","_ref_alt_alleles.txt"), col.names = F, row.names = F) - - write.table(ref_depth_matrix2, file = paste0("freebayes","_ref_depth_bam.txt"), quote=F, row.names=T, sep="\t", col.names=T) - write.table(alt_depth_matrix2, file = paste0("freebayes","_alt_depth_bam.txt"), quote=F, row.names=T, sep="\t", col.names=T) - -RSCRIPT` -[INFO] [08/08/2020 23:08:11.823] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:12.186] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: job id: 20772 -[INFO] [08/08/2020 23:08:12.186] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:15.571] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamCounts4Onemap:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:18.161] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:08:18.170] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:18,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/inputs/874683609/vcf_norm.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-BiallelicNormalization/execution/vcf_norm.vcf: Operation not permitted -[INFO] [08/08/2020 23:08:18.173] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: `vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/inputs/874683609/vcf_norm.vcf --min-alleles 3 --recode --out gatk_multi1 - -vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/inputs/874683609/vcf_norm.vcf --min-alleles 2 --max-alleles 2 --recode --out gatk_bi1 - -Rscript /opt/scripts/split.R gatk_bi1.recode.vcf PT_F PT_M position_multi2.txt - -vcftools --vcf gatk_bi1.recode.vcf --positions position_multi2.txt --recode --out gatk_multi2 - -vcftools --vcf gatk_bi1.recode.vcf --exclude-positions position_multi2.txt --recode --out gatk_bi - -vcf-concat gatk_multi1.recode.vcf gatk_multi2.recode.vcf > gatk_multi.recode.vcf - -vcftools --gzvcf gatk_multi.recode.vcf --chr Chr10 --recode --out gatk_multi_Chr10 - -vcftools --vcf gatk_bi.recode.vcf --chr Chr10 --recode --out gatk_bi_Chr10 - -bgzip gatk_multi.recode.vcf -bgzip gatk_bi_Chr10.recode.vcf -tabix -p vcf gatk_bi_Chr10.recode.vcf.gz -bgzip gatk_multi_Chr10.recode.vcf -bgzip gatk_bi.recode.vcf` -[INFO] [08/08/2020 23:08:18.175] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters:delegated \ - cristaniguti/vcftools@sha256:8510a07715463f02d5cbc57a92aae51b9c6b83bfacf922f61b433e3757644b76 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:19.831] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Starting FreebayesGenotyping.BamDepths2Vcf -[INFO] [08/08/2020 23:08:22.208] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: job id: 21142 -[INFO] [08/08/2020 23:08:22.209] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:24.422] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-EngineJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-BackendJobExecutionActor-SplitFiltVCF.SplitFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(1880a9f4)SplitFiltVCF.SplitFilters:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:28.161] [cromwell-system-akka.dispatchers.engine-dispatcher-17] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:08:28.169] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:28,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/540513273/freebayes_ref_depth_bam.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/freebayes_ref_depth_bam.txt: Operation not permitted -[2020-08-08 23:08:28,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/540513273/freebayes_alt_depth_bam.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/freebayes_alt_depth_bam.txt: Operation not permitted -[2020-08-08 23:08:28,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/540513273/freebayes_ref_alt_alleles.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/freebayes_ref_alt_alleles.txt: Operation not permitted -[2020-08-08 23:08:28,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[INFO] [08/08/2020 23:08:28.175] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz" - } - - allele_file <- paste0("/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/inputs/540513273/freebayes_ref_alt_alleles.txt") - bam_vcf <- make_vcf(vcf_file, depths, allele_file, "freebayes_bam_vcf.vcf") - - bam_vcfR <- read.vcfR(bam_vcf) - save(bam_vcfR, file="freebayes_bam_vcfR.RData") - -RSCRIPT` -[INFO] [08/08/2020 23:08:28.177] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:29.031] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowExecutionActor-SubWorkflow-SplitFiltVCF:-1:1/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1] 1880a9f4-eb6f-4372-8b8b-e190be5b3ac0-SubWorkflowActor-SubWorkflow-SplitFiltVCF:-1:1 [UUID(1880a9f4)]: Workflow SplitFiltVCF complete. Final Outputs: -{ - "SplitFiltVCF.vcf_bi_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi.recode.vcf.gz", - "SplitFiltVCF.vcf_bi_chr_norm_tbi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi", - "SplitFiltVCF.vcf_bi_chr_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz", - "SplitFiltVCF.vcf_multi_chr": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi_Chr10.recode.vcf.gz", - "SplitFiltVCF.vcf_multi_norm": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi.recode.vcf.gz" -} -[INFO] [08/08/2020 23:08:31.052] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.BamCounts (5 shards) -[INFO] [08/08/2020 23:08:32.143] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: job id: 21719 -[INFO] [08/08/2020 23:08:32.144] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:35.041] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.BamDepths2Vcf:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:37.161] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:08:37.288] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:37,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:08:37,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:08:37,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam.bai: Operation not permitted -[2020-08-08 23:08:37,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-1/execution/I_3_55.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:08:37.302] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/-1221296247/I_3_55.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_55_gatk_counts.tsv"` -[INFO] [08/08/2020 23:08:37.306] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:38.192] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Starting FreebayesGenotyping.FiltChr -[INFO] [08/08/2020 23:08:42.154] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: job id: 22312 -[INFO] [08/08/2020 23:08:42.155] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:45.381] [cromwell-system-akka.dispatchers.backend-dispatcher-114] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:1:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:08:49.161] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:08:49.283] [cromwell-system-akka.dispatchers.backend-dispatcher-115] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:08:49,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:08:49,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:08:49,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam.bai: Operation not permitted -[2020-08-08 23:08:49,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-2/execution/I_3_66.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:08:49.289] [cromwell-system-akka.dispatchers.backend-dispatcher-115] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1276719690/I_3_66.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_66_gatk_counts.tsv"` -[INFO] [08/08/2020 23:08:49.291] [cromwell-system-akka.dispatchers.backend-dispatcher-115] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:08:52.135] [cromwell-system-akka.dispatchers.backend-dispatcher-115] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: job id: 22993 -[INFO] [08/08/2020 23:08:52.135] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:08:58.841] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:2:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:2:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:2:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:00.161] [cromwell-system-akka.dispatchers.engine-dispatcher-19] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:09:00.283] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:00,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:09:00,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:09:00,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam.bai: Operation not permitted -[2020-08-08 23:09:00,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-0/execution/I_3_56.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:09:00.289] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/575655112/I_3_56.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "I_3_56_gatk_counts.tsv"` -[INFO] [08/08/2020 23:09:00.291] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:02.217] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: job id: 23621 -[INFO] [08/08/2020 23:09:02.218] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:09:10.681] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:0:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:13.161] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:09:13.284] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:13,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:09:13,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:09:13,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam.bai: Operation not permitted -[2020-08-08 23:09:13,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-4/execution/PT_M.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:09:13.294] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1977784268/PT_M.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "PT_M_gatk_counts.tsv"` -[INFO] [08/08/2020 23:09:13.297] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:17.193] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: job id: 24320 -[INFO] [08/08/2020 23:09:17.193] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:09:25.111] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:4:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:4:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:4:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:28.161] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:09:28.286] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:28,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:09:28,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz.tbi -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi: Operation not permitted -[2020-08-08 23:09:28,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam.bai -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam.bai: Operation not permitted -[2020-08-08 23:09:28,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-CreateAlignmentFromFamilies/CreateAlignmentFromFamilies/12088a9f-28b2-40a2-b329-964946cf15a5/call-RunBwaAlignment/shard-3/execution/PT_F.sorted.bam: Operation not permitted -[INFO] [08/08/2020 23:09:28.294] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: `set -e -java -jar /gatk/picard.jar VcfToIntervalList \ - I=/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz \ - O=interval.list - -/gatk/gatk CollectAllelicCounts \ - --input /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/-520231669/PT_F.sorted.bam \ - --reference /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/inputs/1874442105/Chr09-10.populus.fa \ - --intervals interval.list \ - --output "PT_F_gatk_counts.tsv"` -[INFO] [08/08/2020 23:09:28.296] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3:delegated \ - taniguti/gatk-picard@sha256:80e62140f4d5450650a4cbaf3218e6dba6f8cea80abc8c35dfc80d85069ce944 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:32.210] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: job id: 25154 -[INFO] [08/08/2020 23:09:32.211] [cromwell-system-akka.dispatchers.backend-dispatcher-112] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:09:37.791] [cromwell-system-akka.dispatchers.backend-dispatcher-113] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts:3:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts:3:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts:3:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:40.161] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[INFO] [08/08/2020 23:09:41.381] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.BamCounts4Onemap -[WARN] [08/08/2020 23:09:41.989] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:41,99] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/inputs/-83969994/freebayes_bam_vcf.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/freebayes_bam_vcf.vcf: Operation not permitted -[INFO] [08/08/2020 23:09:41.992] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: `vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/inputs/-83969994/freebayes_bam_vcf.vcf --chr Chr10 --recode --stdout > bam_chr.vcf` -[INFO] [08/08/2020 23:09:41.993] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr:delegated \ - taniguti/vcftools@sha256:3162ee4af077ea7d3b4ae64d94a9651f799fef70b618c56a20586efa44296af6 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:42.232] [cromwell-system-akka.dispatchers.backend-dispatcher-117] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: job id: 25964 -[INFO] [08/08/2020 23:09:42.233] [cromwell-system-akka.dispatchers.backend-dispatcher-117] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:09:47.481] [cromwell-system-akka.dispatchers.backend-dispatcher-119] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-EngineJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-BackendJobExecutionActor-FreebayesGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(7de96f78)FreebayesGenotyping.FiltChr:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:49.162] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:09:49.167] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:49,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/inputs/94296555/I_3_56_gatk_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-0/execution/I_3_56_gatk_counts.tsv: Operation not permitted -[2020-08-08 23:09:49,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/inputs/-1702654804/I_3_55_gatk_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-1/execution/I_3_55_gatk_counts.tsv: Operation not permitted -[2020-08-08 23:09:49,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/inputs/795361133/I_3_66_gatk_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-2/execution/I_3_66_gatk_counts.tsv: Operation not permitted -[2020-08-08 23:09:49,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/inputs/-1001590226/PT_F_gatk_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-3/execution/PT_F_gatk_counts.tsv: Operation not permitted -[2020-08-08 23:09:49,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/inputs/1496425711/PT_M_gatk_counts.tsv -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts/shard-4/execution/PT_M_gatk_counts.tsv: Operation not permitted -[INFO] [08/08/2020 23:09:49.172] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: `R --vanilla --no-save < idx")) - idx <- read.table("idx", stringsAsFactors = F) - idx <- strsplit(idx[,1], ":")[[1]][1] - idx <- as.numeric(idx) -1 - - file.counts <- read.table(paste0(names[1],"_", "gatk","_counts.tsv"), skip = idx, header=T, stringsAsFactors = F) - - ref_depth_matrix2 <- alt_depth_matrix2 <- matrix(NA, nrow = dim(file.counts)[1], ncol = length(names)) - - for(j in 1:length(names)){ - ## From picard tool - - file.counts <- read.table(paste0(names[j],"_", "gatk","_counts.tsv"), skip = idx, header=T, stringsAsFactors = F) - - ref_depth_matrix2[,j] <- file.counts[,3] - alt_depth_matrix2[,j] <- file.counts[,4] - - if(j == 1){ - ref_allele <- file.counts[,5] - alt_allele <- file.counts[,6] - } else { - idx.ref <- which(ref_allele == "N") - idx.alt <- which(alt_allele == "N") - if(length(idx.ref)!=0){ - ref_allele[idx.ref] <- file.counts[idx.ref,5] - } - if(length(idx.alt)!=0){ - alt_allele[idx.alt] <- file.counts[idx.alt,6] - } - } - } - - rownames(ref_depth_matrix2) <- rownames(alt_depth_matrix2) <- paste0(file.counts[,1],"_", file.counts[,2]) - colnames(ref_depth_matrix2) <- colnames(alt_depth_matrix2) <- names - - alleles <- data.frame(file.counts[,1],file.counts[,2], ref_allele, alt_allele) - write.table(alleles, file = paste0("gatk","_ref_alt_alleles.txt"), col.names = F, row.names = F) - - write.table(ref_depth_matrix2, file = paste0("gatk","_ref_depth_bam.txt"), quote=F, row.names=T, sep="\t", col.names=T) - write.table(alt_depth_matrix2, file = paste0("gatk","_alt_depth_bam.txt"), quote=F, row.names=T, sep="\t", col.names=T) - -RSCRIPT` -[INFO] [08/08/2020 23:09:49.173] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:49.541] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-FreebayesGenotyping:-1:1/7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1] 7de96f78-bdf6-425c-83c1-cff22fdd180a-SubWorkflowActor-SubWorkflow-FreebayesGenotyping:-1:1 [UUID(7de96f78)]: Workflow FreebayesGenotyping complete. Final Outputs: -{ - "FreebayesGenotyping.vcf_bi_bam_counts": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/bam_chr.vcf", - "FreebayesGenotyping.alt_bam": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/freebayes_alt_depth_bam.txt", - "FreebayesGenotyping.tbi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz.tbi", - "FreebayesGenotyping.vcf_multi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi.recode.vcf.gz", - "FreebayesGenotyping.ref_bam": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamCounts4Onemap/execution/freebayes_ref_depth_bam.txt", - "FreebayesGenotyping.vcf_bi_bam_counts_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/freebayes_bam_vcf.vcf", - "FreebayesGenotyping.vcf_bi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi.recode.vcf.gz", - "FreebayesGenotyping.vcf": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz" -} -[INFO] [08/08/2020 23:09:52.236] [cromwell-system-akka.dispatchers.backend-dispatcher-116] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: job id: 26313 -[INFO] [08/08/2020 23:09:52.236] [cromwell-system-akka.dispatchers.backend-dispatcher-119] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:09:53.361] [cromwell-system-akka.dispatchers.backend-dispatcher-119] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamCounts4Onemap:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamCounts4Onemap:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:09:55.662] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.BamDepths2Vcf -[INFO] [08/08/2020 23:09:56.161] [cromwell-system-akka.dispatchers.engine-dispatcher-28] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:09:56.170] [cromwell-system-akka.dispatchers.backend-dispatcher-120] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:09:56,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1519075875/gatk_ref_depth_bam.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/gatk_ref_depth_bam.txt: Operation not permitted -[2020-08-08 23:09:56,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1519075875/gatk_alt_depth_bam.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/gatk_alt_depth_bam.txt: Operation not permitted -[2020-08-08 23:09:56,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1519075875/gatk_ref_alt_alleles.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/gatk_ref_alt_alleles.txt: Operation not permitted -[2020-08-08 23:09:56,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[INFO] [08/08/2020 23:09:56.176] [cromwell-system-akka.dispatchers.backend-dispatcher-120] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz" - } - - allele_file <- paste0("/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/inputs/1519075875/gatk_ref_alt_alleles.txt") - bam_vcf <- make_vcf(vcf_file, depths, allele_file, "gatk_bam_vcf.vcf") - - bam_vcfR <- read.vcfR(bam_vcf) - save(bam_vcfR, file="gatk_bam_vcfR.RData") - -RSCRIPT` -[INFO] [08/08/2020 23:09:56.177] [cromwell-system-akka.dispatchers.backend-dispatcher-120] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:09:57.318] [cromwell-system-akka.dispatchers.backend-dispatcher-120] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: job id: 26920 -[INFO] [08/08/2020 23:09:57.318] [cromwell-system-akka.dispatchers.backend-dispatcher-121] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:10:03.821] [cromwell-system-akka.dispatchers.backend-dispatcher-120] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.BamDepths2Vcf:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.BamDepths2Vcf:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:10:07.901] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Starting GatkGenotyping.FiltChr -[INFO] [08/08/2020 23:10:08.161] [cromwell-system-akka.dispatchers.engine-dispatcher-29] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:10:08.175] [cromwell-system-akka.dispatchers.backend-dispatcher-123] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.FiltChr:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.FiltChr:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:10:08,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/inputs/1992542796/gatk_bam_vcf.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/gatk_bam_vcf.vcf: Operation not permitted -[INFO] [08/08/2020 23:10:08.177] [cromwell-system-akka.dispatchers.backend-dispatcher-123] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.FiltChr:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.FiltChr:NA:1]: `vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/inputs/1992542796/gatk_bam_vcf.vcf --chr Chr10 --recode --stdout > bam_chr.vcf` -[INFO] [08/08/2020 23:10:08.179] [cromwell-system-akka.dispatchers.backend-dispatcher-123] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.FiltChr:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.FiltChr:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr:delegated \ - taniguti/vcftools@sha256:3162ee4af077ea7d3b4ae64d94a9651f799fef70b618c56a20586efa44296af6 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:10:12.263] [cromwell-system-akka.dispatchers.backend-dispatcher-123] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.FiltChr:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.FiltChr:NA:1]: job id: 27645 -[INFO] [08/08/2020 23:10:12.264] [cromwell-system-akka.dispatchers.backend-dispatcher-123] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-EngineJobExecutionActor-GatkGenotyping.FiltChr:NA:1/73173054-1ece-47fc-9219-1aeee1913879-BackendJobExecutionActor-GatkGenotyping.FiltChr:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73173054)GatkGenotyping.FiltChr:NA:1]: Status change from - to Done -[INFO] [08/08/2020 23:10:17.081] [cromwell-system-akka.dispatchers.engine-dispatcher-25] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowExecutionActor-SubWorkflow-GatkGenotyping:-1:1/73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1] 73173054-1ece-47fc-9219-1aeee1913879-SubWorkflowActor-SubWorkflow-GatkGenotyping:-1:1 [UUID(73173054)]: Workflow GatkGenotyping complete. Final Outputs: -{ - "GatkGenotyping.vcf_bi_bam_counts": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/bam_chr.vcf", - "GatkGenotyping.ref_bam": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/gatk_ref_depth_bam.txt", - "GatkGenotyping.tbi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz.tbi", - "GatkGenotyping.vcf_multi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi.recode.vcf.gz", - "GatkGenotyping.vcf_bi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi.recode.vcf.gz", - "GatkGenotyping.alt_bam": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamCounts4Onemap/execution/gatk_alt_depth_bam.txt", - "GatkGenotyping.vcf": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz", - "GatkGenotyping.vcf_bi_bam_counts_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/gatk_bam_vcf.vcf" -} -[INFO] [08/08/2020 23:10:19.121] [cromwell-system-akka.dispatchers.engine-dispatcher-60] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-SNPCalling:-1:1/33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1] 33dd1747-4d8c-454c-b25e-88e026690ad6-SubWorkflowActor-SubWorkflow-SNPCalling:-1:1 [UUID(33dd1747)]: Workflow SNPCalling complete. Final Outputs: -{ - "SNPCalling.freebayes_vcf_multi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi.recode.vcf.gz", - "SNPCalling.gatk_vcf_multi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi.recode.vcf.gz", - "SNPCalling.freebayes_vcf_bi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi.recode.vcf.gz", - "SNPCalling.gatk_vcf_bi_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi.recode.vcf.gz", - "SNPCalling.freebayes_vcf": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz", - "SNPCalling.gatk_vcf_bi_bam_count_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-BamDepths2Vcf/execution/gatk_bam_vcf.vcf", - "SNPCalling.gatk_vcf_bi_bam_count": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/bam_chr.vcf", - "SNPCalling.gatk_vcf": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz", - "SNPCalling.freebayes_vcf_bi_bam_count_tot": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-BamDepths2Vcf/execution/freebayes_bam_vcf.vcf", - "SNPCalling.freebayes_vcf_bi_bam_count": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/bam_chr.vcf" -} -[INFO] [08/08/2020 23:10:23.201] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1] ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1 [UUID(ab3ced81)]: Starting Maps.ApplyRandomFilters -[INFO] [08/08/2020 23:10:24.161] [cromwell-system-akka.dispatchers.engine-dispatcher-20] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:10:24.174] [cromwell-system-akka.dispatchers.backend-dispatcher-126] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:10:24,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/-1531147629/bam_chr.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-FiltChr/execution/bam_chr.vcf: Operation not permitted -[2020-08-08 23:10:24,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:10:24,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi_Chr10.recode.vcf.gz: Operation not permitted -[2020-08-08 23:10:24,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/1441162537/bam_chr.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-FiltChr/execution/bam_chr.vcf: Operation not permitted -[INFO] [08/08/2020 23:10:24.179] [cromwell-system-akka.dispatchers.backend-dispatcher-126] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: `vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/1769496760/gatk_bi_Chr10.recode.vcf.gz --recode --stdout > gatk_vcf_filt.vcf - -vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/-586645481/freebayes_bi_Chr10.recode.vcf.gz --recode --stdout > freebayes_vcf_filt.vcf - -vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/1441162537/bam_chr.vcf --recode --stdout > gatk_vcf_bam_counts_filt.vcf - -vcftools --gzvcf /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/inputs/-1531147629/bam_chr.vcf --recode --stdout > freebayes_vcf_bam_counts_filt.vcf` -[INFO] [08/08/2020 23:10:24.181] [cromwell-system-akka.dispatchers.backend-dispatcher-126] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters:delegated \ - taniguti/vcftools@sha256:3162ee4af077ea7d3b4ae64d94a9651f799fef70b618c56a20586efa44296af6 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:10:27.189] [cromwell-system-akka.dispatchers.backend-dispatcher-126] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: job id: 28655 -[INFO] [08/08/2020 23:10:27.190] [cromwell-system-akka.dispatchers.backend-dispatcher-127] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:10:28.201] [cromwell-system-akka.dispatchers.backend-dispatcher-127] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.ApplyRandomFilters:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.ApplyRandomFilters:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.ApplyRandomFilters:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:10:35.441] [cromwell-system-akka.dispatchers.engine-dispatcher-62] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1] ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1 [UUID(ab3ced81)]: Starting Maps.vcf2onemap (2 shards), Maps.Gambis (2 shards) -[INFO] [08/08/2020 23:10:36.161] [cromwell-system-akka.dispatchers.engine-dispatcher-19] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[2020-08-08 23:10:36,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-Gambis/shard-1/inputs/-724097821/freebayes_vcf_bam_counts_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_bam_counts_filt.vcf: Operation not permitted -[2020-08-08 23:10:36,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-Gambis/shard-1/inputs/-724097821/gatk_vcf_bam_counts_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_bam_counts_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:10:36.177] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.Gambis:1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.Gambis:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.Gambis:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:10:43.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.vcf2onemap:1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.vcf2onemap:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.vcf2onemap:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:10:52.175] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.vcf2onemap:0:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.vcf2onemap:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.vcf2onemap:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_bam_counts_filt.vcf: Operation not permitted -[2020-08-08 23:11:03,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-Gambis/shard-0/inputs/-724097821/gatk_vcf_bam_counts_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_bam_counts_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:11:03.173] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.Gambis:0:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.Gambis:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.Gambis:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:11:10.171] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:0:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/inputs/-724097821/freebayes_vcf_filt.vcf" - } - - create_gusmap_report(vcf_file,"freebayes", "vcf", - "gusmap", "PT_F", "PT_M") - -RSCRIPT` -[INFO] [08/08/2020 23:11:10.173] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:11:12.205] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:0:1]: job id: 31298 -[INFO] [08/08/2020 23:11:12.205] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:11:17.262] [cromwell-system-akka.dispatchers.engine-dispatcher-24] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1] 2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1 [UUID(2331697a)]: Starting GusmapMaps.GusmapReport (2 shards) -[INFO] [08/08/2020 23:11:18.161] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-19] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1] ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1 [UUID(ed12800a)]: Starting SupermassaMaps.SupermassaProbs -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-16] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1] 4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1 [UUID(4a19f298)]: Starting SupermassaMaps.SupermassaProbs -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-24] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1] f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1 [UUID(f5bc760c)]: Starting PolyradMaps.PolyradProbs -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-61] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1] 2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1 [UUID(2d78d754)]: Starting UpdogMaps.UpdogProbs -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-62] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1] ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1 [UUID(ba8c60e6)]: Starting PolyradMaps.PolyradProbs -[INFO] [08/08/2020 23:11:18.281] [cromwell-system-akka.dispatchers.engine-dispatcher-21] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1] 40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1 [UUID(40c5b84e)]: Starting UpdogMaps.UpdogProbs -[INFO] [08/08/2020 23:11:21.161] [cromwell-system-akka.dispatchers.engine-dispatcher-17] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:11:21.166] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:11:21.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/inputs/-1726318395/choosed_bam.vcf" - } - - create_gusmap_report(vcf_file,"freebayes", "bam", - "gusmap", "PT_F", "PT_M") - -RSCRIPT` -[INFO] [08/08/2020 23:11:21.169] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:11:22.154] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: job id: 31923 -[INFO] [08/08/2020 23:11:22.154] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:11:26.581] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-SubWorkflowActor-SubWorkflow-GusmapMaps:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/d0fdb378-86bf-4525-9ce5-95f370384635-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d0fdb378)GusmapMaps.GusmapReport:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:11:28.161] [cromwell-system-akka.dispatchers.engine-dispatcher-5] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:11:28.167] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.GlobalError:NA:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.GlobalError:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:11:28,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-GlobalError/inputs/-677202885/freebayes_vcf_onemap.obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:11:28.172] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.GlobalError:NA:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:11:37,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-GQProbs/inputs/-724097821/freebayes_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:11:37.170] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-SubWorkflowActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-EngineJobExecutionActor-SNPCallerMaps.GQProbs:NA:1/231538d0-6466-44c1-a7ec-473c38403a9b-BackendJobExecutionActor-SNPCallerMaps.GQProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(231538d0)SNPCallerMaps.GQProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:11:46.191] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.SupermassaProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:12:52.170] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.UpdogProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:13:04,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/inputs/-724097821/freebayes_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:13:04.176] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.UpdogProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:13:16,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/inputs/-724097821/freebayes_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:13:16.184] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.PolyradProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:13:37,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/inputs/-724097821/freebayes_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/freebayes_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:13:37.210] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.SupermassaProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:15:28.184] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.PolyradProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:15:49.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.GlobalError:NA:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:15:58,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-GQProbs/inputs/-724097821/gatk_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:15:58.196] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-EngineJobExecutionActor-SNPCallerMaps.GQProbs:NA:1/68db031a-9736-481e-8a17-69b0265d1fb9-BackendJobExecutionActor-SNPCallerMaps.GQProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(68db031a)SNPCallerMaps.GQProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[WARN] [08/08/2020 23:16:06.170] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:16:06.174] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/inputs/-724097821/gatk_vcf_filt.vcf" - } - - create_gusmap_report(vcf_file,"gatk", "vcf", - "gusmap", "PT_F", "PT_M") - -RSCRIPT` -[INFO] [08/08/2020 23:16:06.176] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:16:07.150] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: job id: 20730 -[INFO] [08/08/2020 23:16:07.151] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:16:07.442] [cromwell-system-akka.dispatchers.engine-dispatcher-24] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1] 68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1 [UUID(68db031a)]: Starting SNPCallerMaps.FiltersReportEmp, SNPCallerMaps.CheckDepths -[INFO] [08/08/2020 23:16:11.011] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:0:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:16:13.161] [cromwell-system-akka.dispatchers.engine-dispatcher-18] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:16:13.167] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:16:13.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: `R --vanilla --no-save < ", vcf.temp)) - vcf_file <- vcf.temp - } else { - vcf_file <- "/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/inputs/70632964/choosed_bam.vcf" - } - - create_gusmap_report(vcf_file,"gatk", "bam", - "gusmap", "PT_F", "PT_M") - -RSCRIPT` -[INFO] [08/08/2020 23:16:13.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:16:17.161] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: job id: 21124 -[INFO] [08/08/2020 23:16:17.163] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:16:18.471] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-SubWorkflowActor-SubWorkflow-GusmapMaps:0:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-EngineJobExecutionActor-GusmapMaps.GusmapReport:1:1/2331697a-890a-4794-baa0-3f2f6bf7c4dc-BackendJobExecutionActor-GusmapMaps.GusmapReport:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2331697a)GusmapMaps.GusmapReport:1:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:16:21.161] [cromwell-system-akka.dispatchers.engine-dispatcher-57] [akka://cromwell-system/user/SingleWorkflowRunnerActor/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: 1408f921: 1 -[WARN] [08/08/2020 23:16:21.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.PolyradProbs:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:16:21,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/inputs/1119748474/gatk_vcf_onemap.obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:16:21.170] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.PolyradProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:16:40.181] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.SupermassaProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:17:15,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/inputs/-724097821/gatk_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:17:15.209] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.UpdogProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:17:25,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/inputs/-724097821/gatk_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:17:25.174] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.PolyradProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.PolyradProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:17:42.171] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.UpdogProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.UpdogProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[2020-08-08 23:17:52,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/inputs/-724097821/gatk_vcf_filt.vcf -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ApplyRandomFilters/execution/gatk_vcf_filt.vcf: Operation not permitted -[INFO] [08/08/2020 23:17:52.198] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.SupermassaProbs:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.SupermassaProbs:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:18:34.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.FiltersReportEmp:1:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/vcfR_obj.RData: Operation not permitted -[2020-08-08 23:18:43,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-CheckDepths/shard-1/inputs/1989582890/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:18:43.170] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.CheckDepths:1:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/vcfR_obj.RData: Operation not permitted -[2020-08-08 23:18:52,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-CheckDepths/shard-0/inputs/-677202885/freebayes_vcf_onemap.obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:18:52.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.CheckDepths:0:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-1/execution/freebayes_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:00.167] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.FiltersReportEmp:0:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-GQProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:19:07,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-CheckDepths/inputs/907234771/gq_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-GQProbs/execution/gq_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:07.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-SubWorkflowActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-EngineJobExecutionActor-SNPCallerMaps.CheckDepths:NA:1/231538d0-6466-44c1-a7ec-473c38403a9b-BackendJobExecutionActor-SNPCallerMaps.CheckDepths:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(231538d0)SNPCallerMaps.CheckDepths:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-GQProbs/execution/gq_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:15.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-SubWorkflowActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-EngineJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/231538d0-6466-44c1-a7ec-473c38403a9b-BackendJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(231538d0)SNPCallerMaps.FiltersReportEmp:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:24.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.GlobalError:NA:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:34.168] [cromwell-system-akka.dispatchers.backend-dispatcher-131] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.GlobalError:NA:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:42.167] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.GlobalError:NA:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:49.167] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.GlobalError:NA:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:19:58.167] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.GlobalError:NA:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:20:07.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.GlobalError:NA:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:20:15.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.FiltersReportEmp:1:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/vcfR_obj.RData: Operation not permitted -[2020-08-08 23:20:24,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-CheckDepths/shard-1/inputs/750937879/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:20:24.169] [cromwell-system-akka.dispatchers.backend-dispatcher-131] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.CheckDepths:1:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/vcfR_obj.RData: Operation not permitted -[2020-08-08 23:20:30,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-CheckDepths/shard-0/inputs/1119748474/gatk_vcf_onemap.obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:20:30.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.CheckDepths:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-vcf2onemap/shard-0/execution/gatk_vcf_onemap.obj.RData: Operation not permitted -[INFO] [08/08/2020 23:20:36.171] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.FiltersReportEmp:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-GQProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:20:43,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-CheckDepths/inputs/-819896220/gq_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-GQProbs/execution/gq_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:20:43.170] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-EngineJobExecutionActor-SNPCallerMaps.CheckDepths:NA:1/68db031a-9736-481e-8a17-69b0265d1fb9-BackendJobExecutionActor-SNPCallerMaps.CheckDepths:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(68db031a)SNPCallerMaps.CheckDepths:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-GQProbs/execution/gq_onemap_obj.RData: Operation not permitted -[WARN] [08/08/2020 23:20:52.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-EngineJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/68db031a-9736-481e-8a17-69b0265d1fb9-BackendJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(68db031a)SNPCallerMaps.FiltersReportEmp:NA:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:20:52.172] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-EngineJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/68db031a-9736-481e-8a17-69b0265d1fb9-BackendJobExecutionActor-SNPCallerMaps.FiltersReportEmp:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(68db031a)SNPCallerMaps.FiltersReportEmp:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:00.167] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.GlobalError:NA:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:07.169] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.GlobalError:NA:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:15.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.GlobalError:NA:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:22.169] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.GlobalError:NA:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:31.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.GlobalError:NA:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:21:39.167] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.GlobalError:NA:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.GlobalError:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.GlobalError:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[WARN] [08/08/2020 23:21:49.170] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.MapsReportEmp:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:21:49.173] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[WARN] [08/08/2020 23:22:01.170] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.MapsReportEmp:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:22:01.174] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-SubWorkflowActor-SubWorkflow-DefaultMaps:1:1/73656d64-4580-4f96-92a8-20bbddca488d-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/73656d64-4580-4f96-92a8-20bbddca488d-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(73656d64)DefaultMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-FiltersReportEmp/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:22:13.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-SubWorkflowActor-SubWorkflow-SNPCallerMaps:1:1/231538d0-6466-44c1-a7ec-473c38403a9b-EngineJobExecutionActor-SNPCallerMaps.MapsReportEmp:NA:1/231538d0-6466-44c1-a7ec-473c38403a9b-BackendJobExecutionActor-SNPCallerMaps.MapsReportEmp:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(231538d0)SNPCallerMaps.MapsReportEmp:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:22:24.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:22:31,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-CheckDepths/shard-1/inputs/-1294980532/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:22:31.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.CheckDepths:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[WARN] [08/08/2020 23:22:39.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.CheckDepths:0:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.CheckDepths:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:22:39,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-CheckDepths/shard-0/inputs/-709285901/supermassa_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:22:39.176] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.CheckDepths:0:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:22:49.167] [cromwell-system-akka.dispatchers.backend-dispatcher-131] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:22:55.173] [cromwell-system-akka.dispatchers.backend-dispatcher-131] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:23:04.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:23:12,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-CheckDepths/shard-0/inputs/-158466427/updog_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[WARN] [08/08/2020 23:23:12.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.CheckDepths:0:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.CheckDepths:0:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:23:12.174] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.CheckDepths:0:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:23:19,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-CheckDepths/shard-1/inputs/1120441871/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:23:19.168] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.CheckDepths:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:23:27.171] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:23:34.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:23:43,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-CheckDepths/shard-0/inputs/-1674593557/updog_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:23:43.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.CheckDepths:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:23:52,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-CheckDepths/shard-1/inputs/1365141097/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:23:52.171] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.CheckDepths:1:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[WARN] [08/08/2020 23:24:00.172] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.CheckDepths:1:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.CheckDepths:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[2020-08-08 23:24:00,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-CheckDepths/shard-1/inputs/-1514039211/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:24:00.179] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.CheckDepths:1:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:24:06,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-CheckDepths/shard-0/inputs/942932023/polyrad_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:24:06.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.CheckDepths:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:24:16.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:24:24.167] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:24:31.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:24:39,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-CheckDepths/shard-1/inputs/1464433021/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:24:39.174] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.CheckDepths:1:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:24:45,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-CheckDepths/shard-0/inputs/-240814428/supermassa_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:24:45.169] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.CheckDepths:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:24:51.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:24:58,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-CheckDepths/shard-1/inputs/911745616/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:24:58.170] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.CheckDepths:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:25:06,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-CheckDepths/shard-0/inputs/-1167149668/polyrad_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:25:06.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.CheckDepths:0:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:25:16.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:25:22.169] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:25:30.167] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:25:40.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-SubWorkflowActor-SubWorkflow-DefaultMaps:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-EngineJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/e2a1ef38-7243-4aab-bac2-3564e3ef3b37-BackendJobExecutionActor-DefaultMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e2a1ef38)DefaultMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-FiltersReportEmp/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:25:49.167] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-SubWorkflowActor-SubWorkflow-SNPCallerMaps:0:1/68db031a-9736-481e-8a17-69b0265d1fb9-EngineJobExecutionActor-SNPCallerMaps.MapsReportEmp:NA:1/68db031a-9736-481e-8a17-69b0265d1fb9-BackendJobExecutionActor-SNPCallerMaps.MapsReportEmp:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(68db031a)SNPCallerMaps.MapsReportEmp:NA:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:25:58,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-CheckDepths/shard-1/inputs/200090238/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:25:58.169] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.CheckDepths:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:26:06,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-CheckDepths/shard-0/inputs/-1753629906/polyrad_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:26:06.169] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.CheckDepths:0:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:26:13.166] [cromwell-system-akka.dispatchers.backend-dispatcher-128] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:26:22.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:26:31.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:26:39,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-CheckDepths/shard-1/inputs/1753626225/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:26:39.168] [cromwell-system-akka.dispatchers.backend-dispatcher-130] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.CheckDepths:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:26:45,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-CheckDepths/shard-0/inputs/1804769688/supermassa_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:26:45.167] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.CheckDepths:0:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:26:54.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:27:00.167] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:27:09.167] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:27:19,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-CheckDepths/shard-0/inputs/-2026494939/updog_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:27:19.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.CheckDepths:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:27:28,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-CheckDepths/shard-1/inputs/-953867153/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:27:28.168] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.CheckDepths:1:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:27:36,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-CheckDepths/shard-0/inputs/-1865072748/polyrad_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:27:36.170] [cromwell-system-akka.dispatchers.backend-dispatcher-132] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.CheckDepths:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:27:43,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-CheckDepths/shard-1/inputs/612137304/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:27:43.169] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.CheckDepths:1:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:27:51.168] [cromwell-system-akka.dispatchers.backend-dispatcher-129] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-PolyradProbs/execution/polyrad_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:28:00.168] [cromwell-system-akka.dispatchers.backend-dispatcher-131] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:28:10.237] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:28:19.169] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:28:28,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-CheckDepths/shard-1/inputs/-131705865/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:28:28.167] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.CheckDepths:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-UpdogProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:28:37,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-CheckDepths/shard-0/inputs/-1861426275/updog_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-UpdogProbs/execution/updog_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:28:37.167] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.CheckDepths:0:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:28:45.166] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.FiltersReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:28:53,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-CheckDepths/shard-1/inputs/1821739461/onemap_obj_globalError.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-GlobalError/execution/onemap_obj_globalError.RData: Operation not permitted -[INFO] [08/08/2020 23:28:53.170] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.CheckDepths:1:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.CheckDepths:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.CheckDepths:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/execution/vcfR.RData: Operation not permitted -[2020-08-08 23:29:01,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-CheckDepths/shard-0/inputs/1717576428/supermassa_onemap_obj.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:29:01.169] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.CheckDepths:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.CheckDepths:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.CheckDepths:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-SupermassaProbs/execution/supermassa_onemap_obj.RData: Operation not permitted -[INFO] [08/08/2020 23:29:09.167] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.FiltersReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.FiltersReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[WARN] [08/08/2020 23:29:18.166] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.MapsReportEmp:1:1]: Unrecognized runtime attribute keys: mem, cpu, time -[INFO] [08/08/2020 23:29:18.169] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:29:28.170] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/cd8d6b1b-812e-4549-8357-9897f6de42ae-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(cd8d6b1b)SupermassaMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:29:39.167] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:29:49.167] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/e0e6f37b-562d-4eba-808f-bf8ffb429a5b-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(e0e6f37b)UpdogMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:01.232] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:10.167] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/ce9cdb98-ef15-417f-ba96-4f9842dc8e02-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ce9cdb98)UpdogMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:19.170] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:28.167] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/8bfdea08-e209-4a31-bd1c-2def3cf7c425-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(8bfdea08)PolyradMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:37.168] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:45.168] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/d06d7775-e752-4b4b-8c6e-3215b51e4a38-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(d06d7775)SupermassaMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:30:55.168] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:07.167] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowActor-SubWorkflow-ScatterAt88_13:1:1/1d231265-5d74-489c-886b-48c40365680b-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(74df0a4b)PolyradMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:16.167] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:25.168] [cromwell-system-akka.dispatchers.backend-dispatcher-136] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-SubWorkflowActor-SubWorkflow-PolyradMaps:1:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/f5bc760c-3f5b-4cba-adad-048b5b247d48-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(f5bc760c)PolyradMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:37.167] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:49.169] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-SubWorkflowActor-SubWorkflow-SupermassaMaps:1:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/ed12800a-242f-4a4a-91fe-8cf721b7beb6-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ed12800a)SupermassaMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:31:58.167] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:06.168] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-SubWorkflowActor-SubWorkflow-UpdogMaps:0:1/2d78d754-629e-48c8-88db-a6142fa937b8-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/2d78d754-629e-48c8-88db-a6142fa937b8-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(2d78d754)UpdogMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:16.192] [cromwell-system-akka.dispatchers.backend-dispatcher-135] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:25.169] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-SubWorkflowActor-SubWorkflow-PolyradMaps:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-EngineJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/ba8c60e6-606b-4596-8337-5ab3e71c7d45-BackendJobExecutionActor-PolyradMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ba8c60e6)PolyradMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:34.168] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:43.167] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-SubWorkflowActor-SubWorkflow-UpdogMaps:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-EngineJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5-BackendJobExecutionActor-UpdogMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(40c5b84e)UpdogMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-FiltersReportEmp/shard-1/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:32:54.167] [cromwell-system-akka.dispatchers.backend-dispatcher-134] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:1:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.MapsReportEmp:1:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-FiltersReportEmp/shard-0/execution/onemap_obj_filtered.RData: Operation not permitted -[INFO] [08/08/2020 23:33:01.167] [cromwell-system-akka.dispatchers.backend-dispatcher-133] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowExecutionActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowActor-SubWorkflow-ScatterAt88_13:0:1/579d8496-5804-4917-9f34-469a41ee817f-SubWorkflowExecutionActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-SubWorkflowActor-SubWorkflow-SupermassaMaps:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-EngineJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/4a19f298-530f-45c0-95aa-f63ee432ef83-BackendJobExecutionActor-SupermassaMaps.MapsReportEmp:0:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(4a19f298)SupermassaMaps.MapsReportEmp:0:1]: `R --vanilla --no-save < /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-0/execution/times_gatk_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,16] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1222482434/times_gatk_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-1/execution/times_gatk_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1114430316/times_freebayes_vcf_default.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-0/execution/times_freebayes_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1383585621/times_freebayes_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-1/execution/times_freebayes_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/times_gatk_vcf_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/times_gatk_vcf_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/times_gatk_bam_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/times_gatk_bam_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/times_freebayes_vcf_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/times_freebayes_vcf_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/times_freebayes_bam_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/times_freebayes_bam_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1407506294/gatk_vcf_supermassa_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-CheckDepths/shard-0/execution/gatk_vcf_supermassa_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,17] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1090509643/gatk_vcf_supermassa0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-CheckDepths/shard-1/execution/gatk_vcf_supermassa0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1352296758/gatk_bam_supermassa_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-CheckDepths/shard-0/execution/gatk_bam_supermassa_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-444654601/gatk_bam_supermassa0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-CheckDepths/shard-1/execution/gatk_bam_supermassa0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1465917374/freebayes_vcf_supermassa_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-CheckDepths/shard-0/execution/freebayes_vcf_supermassa_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1032098563/freebayes_vcf_supermassa0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-CheckDepths/shard-1/execution/freebayes_vcf_supermassa0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/231494161/freebayes_bam_supermassa_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-CheckDepths/shard-0/execution/freebayes_bam_supermassa_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1565457198/freebayes_bam_supermassa0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-CheckDepths/shard-1/execution/freebayes_bam_supermassa0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/map_gatk_vcf_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/map_gatk_vcf_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/map_gatk_bam_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/map_gatk_bam_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/map_freebayes_vcf_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/map_freebayes_vcf_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/map_freebayes_bam_gusmap.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/map_freebayes_bam_gusmap.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1275533503/map_gatk_vcf_default.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,18] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1222482434/map_gatk_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1114430316/map_freebayes_vcf_default.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1383585621/map_freebayes_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-762721667/filters_gatk_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-FiltersReportEmp/shard-0/execution/filters_gatk_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1735294270/filters_gatk_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-FiltersReportEmp/shard-1/execution/filters_gatk_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-2129390255/filters_gatk_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-FiltersReportEmp/shard-0/execution/filters_gatk_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/368625682/filters_gatk_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-FiltersReportEmp/shard-1/execution/filters_gatk_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1990515259/filters_freebayes_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-FiltersReportEmp/shard-0/execution/filters_freebayes_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/507500678/filters_freebayes_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-FiltersReportEmp/shard-1/execution/filters_freebayes_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1266123434/filters_freebayes_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-FiltersReportEmp/shard-0/execution/filters_freebayes_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1231892503/filters_freebayes_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-FiltersReportEmp/shard-1/execution/filters_freebayes_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/map_gatk_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/map_gatk_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,19] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/map_gatk_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-0/execution/map_gatk_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/map_gatk_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-1/execution/map_gatk_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/map_freebayes_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/map_freebayes_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/map_freebayes_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/map_freebayes_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/31287579/filters_gatk_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-FiltersReportEmp/execution/filters_gatk_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1013045108/filters_freebayes_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-FiltersReportEmp/execution/filters_freebayes_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1275533503/map_gatk_vcf_default.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_default.RData: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1222482434/map_gatk_vcf_default0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_default0.05.RData: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1114430316/map_freebayes_vcf_default.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_default.RData: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1383585621/map_freebayes_vcf_default0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_default0.05.RData: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/619631901/gatk_vcf_polyrad_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-CheckDepths/shard-0/execution/gatk_vcf_polyrad_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,20] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1177319458/gatk_vcf_polyrad0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-CheckDepths/shard-1/execution/gatk_vcf_polyrad0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-875628477/gatk_bam_polyrad_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-CheckDepths/shard-0/execution/gatk_bam_polyrad_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1622387460/gatk_bam_polyrad0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-CheckDepths/shard-1/execution/gatk_bam_polyrad0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/500672282/freebayes_vcf_polyrad_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-CheckDepths/shard-0/execution/freebayes_vcf_polyrad_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1296279077/freebayes_vcf_polyrad0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-CheckDepths/shard-1/execution/freebayes_vcf_polyrad0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1225914859/freebayes_bam_polyrad_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-CheckDepths/shard-0/execution/freebayes_bam_polyrad_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1272101078/freebayes_bam_polyrad0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-CheckDepths/shard-1/execution/freebayes_bam_polyrad0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/302420956/gatk_vcf_default_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-CheckDepths/shard-0/execution/gatk_vcf_default_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1494530403/gatk_vcf_default0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-CheckDepths/shard-1/execution/gatk_vcf_default0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-2052716049/freebayes_vcf_default_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-CheckDepths/shard-0/execution/freebayes_vcf_default_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/445299888/freebayes_vcf_default0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-CheckDepths/shard-1/execution/freebayes_vcf_default0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/map_gatk_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/map_gatk_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,21] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/map_gatk_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-0/execution/map_gatk_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/map_gatk_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-1/execution/map_gatk_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/map_freebayes_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/map_freebayes_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/map_freebayes_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/map_freebayes_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/map_gatk_vcf_polyrad.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_polyrad.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/map_gatk_vcf_polyrad0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_polyrad0.05.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/map_gatk_bam_polyrad.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-0/execution/map_gatk_bam_polyrad.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/map_gatk_bam_polyrad0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-1/execution/map_gatk_bam_polyrad0.05.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/map_freebayes_vcf_polyrad.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_polyrad.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/map_freebayes_vcf_polyrad0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_polyrad0.05.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/map_freebayes_bam_polyrad.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_polyrad.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/map_freebayes_bam_polyrad0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_polyrad0.05.RData: Operation not permitted -[2020-08-08 23:33:20,22] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/map_gatk_vcf_updog.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_updog.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/map_gatk_vcf_updog0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_updog0.05.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/map_gatk_bam_updog.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-0/execution/map_gatk_bam_updog.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/map_gatk_bam_updog0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-1/execution/map_gatk_bam_updog0.05.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/map_freebayes_vcf_updog.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_updog.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/map_freebayes_vcf_updog0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_updog0.05.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/map_freebayes_bam_updog.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_updog.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/map_freebayes_bam_updog0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_updog0.05.RData: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/times_gatk_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-0/execution/times_gatk_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/times_gatk_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-1/execution/times_gatk_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/times_gatk_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-0/execution/times_gatk_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/times_gatk_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-1/execution/times_gatk_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/times_freebayes_vcf_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-0/execution/times_freebayes_vcf_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/times_freebayes_vcf_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-1/execution/times_freebayes_vcf_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/times_freebayes_bam_supermassa.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-0/execution/times_freebayes_bam_supermassa.txt: Operation not permitted -[2020-08-08 23:33:20,23] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/times_freebayes_bam_supermassa0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-1/execution/times_freebayes_bam_supermassa0.05.txt: Operation not permitted -[2020-08-08 23:33:20,24] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/889340141/times_gatk_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-MapsReportEmp/execution/times_gatk_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,24] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-136175844/times_freebayes_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-MapsReportEmp/execution/times_freebayes_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,24] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1058253805/filters_gatk_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-FiltersReportEmp/shard-0/execution/filters_gatk_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,24] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1439762132/filters_gatk_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-FiltersReportEmp/shard-1/execution/filters_gatk_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,24] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1352490613/filters_gatk_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-FiltersReportEmp/shard-0/execution/filters_gatk_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1145525324/filters_gatk_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-FiltersReportEmp/shard-1/execution/filters_gatk_bam_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1041995865/filters_freebayes_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-FiltersReportEmp/shard-0/execution/filters_freebayes_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-754955494/filters_freebayes_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-FiltersReportEmp/shard-1/execution/filters_freebayes_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1765374349/filters_freebayes_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-FiltersReportEmp/shard-0/execution/filters_freebayes_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/732641588/filters_freebayes_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-FiltersReportEmp/shard-1/execution/filters_freebayes_bam_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/map_gatk_vcf_gusmap.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-0/execution/map_gatk_vcf_gusmap.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/map_gatk_bam_gusmap.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-0/GusmapMaps/2331697a-890a-4794-baa0-3f2f6bf7c4dc/call-GusmapReport/shard-1/execution/map_gatk_bam_gusmap.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/map_freebayes_vcf_gusmap.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-0/execution/map_freebayes_vcf_gusmap.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/map_freebayes_bam_gusmap.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-GusmapMaps/shard-1/GusmapMaps/d0fdb378-86bf-4525-9ce5-95f370384635/call-GusmapReport/shard-1/execution/map_freebayes_bam_gusmap.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/map_gatk_vcf_supermassa.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_supermassa.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/map_gatk_vcf_supermassa0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-0/SupermassaMaps/4a19f298-530f-45c0-95aa-f63ee432ef83/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_supermassa0.05.RData: Operation not permitted -[2020-08-08 23:33:20,26] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/map_gatk_bam_supermassa.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-0/execution/map_gatk_bam_supermassa.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/map_gatk_bam_supermassa0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-SupermassaMaps/shard-1/SupermassaMaps/ed12800a-242f-4a4a-91fe-8cf721b7beb6/call-MapsReportEmp/shard-1/execution/map_gatk_bam_supermassa0.05.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/map_freebayes_vcf_supermassa.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_supermassa.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/map_freebayes_vcf_supermassa0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-0/SupermassaMaps/d06d7775-e752-4b4b-8c6e-3215b51e4a38/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_supermassa0.05.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/map_freebayes_bam_supermassa.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_supermassa.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/map_freebayes_bam_supermassa0.05.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-SupermassaMaps/shard-1/SupermassaMaps/cd8d6b1b-812e-4549-8357-9897f6de42ae/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_supermassa0.05.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/889340141/map_gatk_vcf_SNPCaller.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-MapsReportEmp/execution/map_gatk_vcf_SNPCaller.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-136175844/map_freebayes_vcf_SNPCaller.RData -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-MapsReportEmp/execution/map_freebayes_vcf_SNPCaller.RData: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-771414008/gatk_vcf_SNPCaller_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-CheckDepths/execution/gatk_vcf_SNPCaller_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1783940599/freebayes_vcf_SNPCaller_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-CheckDepths/execution/freebayes_vcf_SNPCaller_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/times_gatk_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-0/execution/times_gatk_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/times_gatk_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-MapsReportEmp/shard-1/execution/times_gatk_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/times_gatk_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-0/execution/times_gatk_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/times_gatk_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-MapsReportEmp/shard-1/execution/times_gatk_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/times_freebayes_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-0/execution/times_freebayes_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/times_freebayes_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-MapsReportEmp/shard-1/execution/times_freebayes_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,27] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/times_freebayes_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-0/execution/times_freebayes_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/times_freebayes_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-MapsReportEmp/shard-1/execution/times_freebayes_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/times_gatk_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-0/execution/times_gatk_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/times_gatk_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-1/execution/times_gatk_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/times_gatk_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-0/execution/times_gatk_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/times_gatk_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-1/execution/times_gatk_bam_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/times_freebayes_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-0/execution/times_freebayes_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/times_freebayes_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-1/execution/times_freebayes_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/times_freebayes_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-0/execution/times_freebayes_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/times_freebayes_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-1/execution/times_freebayes_bam_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1980325269/filters_gatk_vcf_default.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-FiltersReportEmp/shard-0/execution/filters_gatk_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/517690668/filters_gatk_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-0/DefaultMaps/e2a1ef38-7243-4aab-bac2-3564e3ef3b37/call-FiltersReportEmp/shard-1/execution/filters_gatk_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-33750984/filters_freebayes_vcf_default.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-FiltersReportEmp/shard-0/execution/filters_freebayes_vcf_default.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1830702343/filters_freebayes_vcf_default0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-DefaultMaps/shard-1/DefaultMaps/73656d64-4580-4f96-92a8-20bbddca488d/call-FiltersReportEmp/shard-1/execution/filters_freebayes_vcf_default0.05.txt: Operation not permitted -[2020-08-08 23:33:20,28] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1478330060/gatk_vcf_updog_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-CheckDepths/shard-0/execution/gatk_vcf_updog_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1019685877/gatk_vcf_updog0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-CheckDepths/shard-1/execution/gatk_vcf_updog0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1667260228/gatk_bam_updog_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-CheckDepths/shard-0/execution/gatk_bam_updog_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/830755709/gatk_bam_updog0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-CheckDepths/shard-1/execution/gatk_bam_updog0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/337584430/freebayes_vcf_updog_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-CheckDepths/shard-0/execution/freebayes_vcf_updog_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1459366929/freebayes_vcf_updog0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-CheckDepths/shard-1/execution/freebayes_vcf_updog0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1337308460/freebayes_bam_updog_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-CheckDepths/shard-0/execution/freebayes_bam_updog_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1160707477/freebayes_bam_updog0.05_vcf_depths.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-CheckDepths/shard-1/execution/freebayes_bam_updog0.05_vcf_depths.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/889340141/map_gatk_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-0/SNPCallerMaps/68db031a-9736-481e-8a17-69b0265d1fb9/call-MapsReportEmp/execution/map_gatk_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-136175844/map_freebayes_vcf_SNPCaller.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-SNPCallerMaps/shard-1/SNPCallerMaps/231538d0-6466-44c1-a7ec-473c38403a9b/call-MapsReportEmp/execution/map_freebayes_vcf_SNPCaller.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1643774410/filters_gatk_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-FiltersReportEmp/shard-0/execution/filters_gatk_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-153176949/filters_gatk_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-0/PolyradMaps/ba8c60e6-606b-4596-8337-5ab3e71c7d45/call-FiltersReportEmp/shard-1/execution/filters_gatk_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,29] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/26207844/filters_gatk_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-FiltersReportEmp/shard-0/execution/filters_gatk_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1770743515/filters_gatk_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-PolyradMaps/shard-1/PolyradMaps/f5bc760c-3f5b-4cba-adad-048b5b247d48/call-FiltersReportEmp/shard-1/execution/filters_gatk_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/245753325/filters_freebayes_vcf_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-FiltersReportEmp/shard-0/execution/filters_freebayes_vcf_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1551198034/filters_freebayes_vcf_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-0/PolyradMaps/8bfdea08-e209-4a31-bd1c-2def3cf7c425/call-FiltersReportEmp/shard-1/execution/filters_freebayes_vcf_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-953504814/filters_freebayes_bam_polyrad.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-FiltersReportEmp/shard-0/execution/filters_freebayes_bam_polyrad.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1544511123/filters_freebayes_bam_polyrad0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-PolyradMaps/shard-1/PolyradMaps/74df0a4b-a4a8-4bfb-a5eb-b094aef7366c/call-FiltersReportEmp/shard-1/execution/filters_freebayes_bam_polyrad0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/map_gatk_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-0/execution/map_gatk_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/map_gatk_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-0/UpdogMaps/2d78d754-629e-48c8-88db-a6142fa937b8/call-MapsReportEmp/shard-1/execution/map_gatk_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/map_gatk_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-0/execution/map_gatk_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/map_gatk_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-0/ScatterAt88_13/579d8496-5804-4917-9f34-469a41ee817f/call-UpdogMaps/shard-1/UpdogMaps/40c5b84e-1dcc-4cfb-8dd7-48cfa8f6bee5/call-MapsReportEmp/shard-1/execution/map_gatk_bam_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/map_freebayes_vcf_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-0/execution/map_freebayes_vcf_updog.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/map_freebayes_vcf_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-0/UpdogMaps/ce9cdb98-ef15-417f-ba96-4f9842dc8e02/call-MapsReportEmp/shard-1/execution/map_freebayes_vcf_updog0.05.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/map_freebayes_bam_updog.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-0/execution/map_freebayes_bam_updog.txt: Operation not permitted -[2020-08-08 23:33:20,30] [warn] Localization via hard link has failed: /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/map_freebayes_bam_updog0.05.txt -> /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-ScatterAt88_13/shard-1/ScatterAt88_13/1d231265-5d74-489c-886b-48c40365680b/call-UpdogMaps/shard-1/UpdogMaps/e0e6f37b-562d-4eba-808f-bf8ffb429a5b/call-MapsReportEmp/shard-1/execution/map_freebayes_bam_updog0.05.txt: Operation not permitted -[INFO] [08/08/2020 23:33:20.335] [cromwell-system-akka.dispatchers.backend-dispatcher-137] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.JointReports:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.JointReports:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.JointReports:NA:1]: `R --vanilla --no-save < temp_map1") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/map_gatk_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/map_gatk_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/map_gatk_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/map_gatk_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/map_freebayes_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/map_freebayes_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/map_freebayes_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/map_freebayes_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/map_gatk_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/map_gatk_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/map_gatk_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/map_gatk_bam_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/map_freebayes_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/map_freebayes_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/map_freebayes_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/map_freebayes_bam_polyrad0.05.txt > temp_map2") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/map_gatk_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/map_gatk_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/map_gatk_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/map_gatk_bam_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/map_freebayes_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/map_freebayes_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/map_freebayes_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/map_freebayes_bam_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/map_gatk_vcf_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/map_gatk_bam_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/map_freebayes_vcf_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/map_freebayes_bam_gusmap.txt > temp_map3") - system("cat temp_map1 temp_map2 temp_map3 > all_maps.txt") - - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1980325269/filters_gatk_vcf_default.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/517690668/filters_gatk_vcf_default0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-33750984/filters_freebayes_vcf_default.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1830702343/filters_freebayes_vcf_default0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/31287579/filters_gatk_vcf_SNPCaller.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1013045108/filters_freebayes_vcf_SNPCaller.txt > temp_filters1") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1058253805/filters_gatk_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1439762132/filters_gatk_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1352490613/filters_gatk_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1145525324/filters_gatk_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1041995865/filters_freebayes_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-754955494/filters_freebayes_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1765374349/filters_freebayes_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/732641588/filters_freebayes_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1643774410/filters_gatk_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-153176949/filters_gatk_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/26207844/filters_gatk_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1770743515/filters_gatk_bam_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/245753325/filters_freebayes_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1551198034/filters_freebayes_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-953504814/filters_freebayes_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1544511123/filters_freebayes_bam_polyrad0.05.txt > temp_filters2") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-762721667/filters_gatk_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1735294270/filters_gatk_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-2129390255/filters_gatk_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/368625682/filters_gatk_bam_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1990515259/filters_freebayes_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/507500678/filters_freebayes_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1266123434/filters_freebayes_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1231892503/filters_freebayes_bam_supermassa0.05.txt > temp_filters3") - system("cat temp_filters1 temp_filters2 temp_filters3 > all_filters.txt") - - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/302420956/gatk_vcf_default_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1494530403/gatk_vcf_default0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-2052716049/freebayes_vcf_default_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/445299888/freebayes_vcf_default0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-771414008/gatk_vcf_SNPCaller_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1783940599/freebayes_vcf_SNPCaller_vcf_depths.txt > temp_errors1") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1478330060/gatk_vcf_updog_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1019685877/gatk_vcf_updog0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1667260228/gatk_bam_updog_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/830755709/gatk_bam_updog0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/337584430/freebayes_vcf_updog_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1459366929/freebayes_vcf_updog0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1337308460/freebayes_bam_updog_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1160707477/freebayes_bam_updog0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/619631901/gatk_vcf_polyrad_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1177319458/gatk_vcf_polyrad0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-875628477/gatk_bam_polyrad_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1622387460/gatk_bam_polyrad0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/500672282/freebayes_vcf_polyrad_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1296279077/freebayes_vcf_polyrad0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1225914859/freebayes_bam_polyrad_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1272101078/freebayes_bam_polyrad0.05_vcf_depths.txt > temp_errors2") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1407506294/gatk_vcf_supermassa_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1090509643/gatk_vcf_supermassa0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1352296758/gatk_bam_supermassa_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-444654601/gatk_bam_supermassa0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1465917374/freebayes_vcf_supermassa_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1032098563/freebayes_vcf_supermassa0.05_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/231494161/freebayes_bam_supermassa_vcf_depths.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1565457198/freebayes_bam_supermassa0.05_vcf_depths.txt > temp_errors3") - system("cat temp_errors1 temp_errors2 temp_errors3 > all_errors.txt") - - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1275533503/times_gatk_vcf_default.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1222482434/times_gatk_vcf_default0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1114430316/times_freebayes_vcf_default.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1383585621/times_freebayes_vcf_default0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/889340141/times_gatk_vcf_SNPCaller.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-136175844/times_freebayes_vcf_SNPCaller.txt > temp_times1") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/times_gatk_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/times_gatk_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/times_gatk_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/times_gatk_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/times_freebayes_vcf_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/times_freebayes_vcf_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/times_freebayes_bam_updog.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/times_freebayes_bam_updog0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/times_gatk_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/times_gatk_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/times_gatk_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/times_gatk_bam_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/times_freebayes_vcf_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/times_freebayes_vcf_polyrad0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/times_freebayes_bam_polyrad.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/times_freebayes_bam_polyrad0.05.txt > temp_times2") - system("cat /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/times_gatk_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/times_gatk_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/times_gatk_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/times_gatk_bam_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/times_freebayes_vcf_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/times_freebayes_vcf_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/times_freebayes_bam_supermassa.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/times_freebayes_bam_supermassa0.05.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/times_gatk_vcf_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/times_gatk_bam_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/times_freebayes_vcf_gusmap.txt /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/times_freebayes_bam_gusmap.txt > temp_times3") - system("cat temp_times1 temp_times2 temp_times3 > all_times.txt") - - # RDatas need to be load - system("cp /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1275533503/map_gatk_vcf_default.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1222482434/map_gatk_vcf_default0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1114430316/map_freebayes_vcf_default.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1383585621/map_freebayes_vcf_default0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/889340141/map_gatk_vcf_SNPCaller.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-136175844/map_freebayes_vcf_SNPCaller.RData .") - system("cp /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1114691225/map_gatk_vcf_updog.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-682260134/map_gatk_vcf_updog0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-58573791/map_gatk_bam_updog.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1855525150/map_gatk_bam_updog0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1843173357/map_freebayes_vcf_updog.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/654842580/map_freebayes_vcf_updog0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-802504647/map_freebayes_bam_updog.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1695511290/map_freebayes_bam_updog0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1378493374/map_gatk_vcf_polyrad.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1119522563/map_gatk_vcf_polyrad0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/490327528/map_gatk_bam_polyrad.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1306623831/map_gatk_bam_polyrad0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/265429759/map_freebayes_vcf_polyrad.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1531521600/map_freebayes_vcf_polyrad0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1127436486/map_freebayes_bam_polyrad.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1370579451/map_freebayes_bam_polyrad0.05.RData .") - system("cp /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/456853615/map_gatk_vcf_supermassa.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1340097744/map_gatk_vcf_supermassa0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1662202341/map_gatk_bam_supermassa.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/835813596/map_gatk_bam_supermassa0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/158380583/map_freebayes_vcf_supermassa.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1638570776/map_freebayes_vcf_supermassa0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-716706762/map_freebayes_bam_supermassa.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1781309175/map_freebayes_bam_supermassa0.05.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-1385948762/map_gatk_vcf_gusmap.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1112067175/map_gatk_bam_gusmap.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/1000008920/map_freebayes_vcf_gusmap.RData /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/inputs/-796942439/map_freebayes_bam_gusmap.RData .") - -library(tidyr) -library(largeList) -library(data.table) -source("/opt/scripts/functions_empirical.R") - -Genocall <- c("default", "SNPCaller", "updog", "supermassa", "polyrad", "gusmap", - "default0.05", "updog0.05", "supermassa0.05", "polyrad0.05") -fake <- c(TRUE, FALSE) -CountsFrom <- c("vcf", "bam") -SNPCall <- c("gatk", "freebayes") - - df <- data.frame(SNPCall, CountsFrom, Genocall) - df <- tidyr::expand(df, SNPCall, CountsFrom, Genocall) - df <- as.data.frame(df) - df <- df[-which((df[,3] == "default" | df[,3] == "default0.05" | df[,3] == "SNPCaller" ) & df[,2] == "bam"),] - RDatas_names <- paste0("map_",df[,1],"_",df[,2], "_", df[,3],".RData") - - all_RDatas <- list() - for(i in 1:length(RDatas_names)){ - map_temp <- load(RDatas_names[i]) - all_RDatas[[i]] <- get(map_temp) - } - - names(all_RDatas) <- RDatas_names - gusmap_RDatas <- all_RDatas[grep("gusmap", names(all_RDatas))] - RDatas <- all_RDatas[-grep("gusmap", names(all_RDatas))] - - # Converting OneMap sequencig objects to list. LargeList do not accept other class - # Also because of this gusmap is separated, because the developers worked with enviroments, not classes - - for(i in 1:length(RDatas)){ - class(RDatas[[i]]) <- "list" - } - - saveList(RDatas, file = "sequences_emp.llo", append=FALSE, compress=TRUE) - - new_names <- names(all_RDatas) - saveRDS(new_names, file = "names.rds") - save(gusmap_RDatas, file = "gusmap_RDatas.RData") - - all_errors <- fread("all_errors.txt") - colnames(all_errors) <- c("SNPCall", "CountsFrom", "GenoCall", "mks", "ind", "alt", "ref", - "gt.onemap", "gt.vcf", "A", "AB", "BA", "B") - all_errors <- fix_genocall_names(all_errors) - saveRDS(all_errors, "data1_depths_geno_prob.rds") - - all_filters <- fread("all_filters.txt") - colnames(all_filters) <- c("CountsFrom", "SNPCall", "GenoCall", - "miss", "n_markers", "n_markers_selected_chr", - "selected_chr_no_dist", "distorted_markers", - "redundant_markers", "non-grouped_markers") - all_filters <- fix_genocall_names(all_filters) - saveRDS(all_filters, "data3_filters.rds") - - all_maps <- fread("all_maps.txt") - colnames(all_maps) <- c("CountsFrom", "SNPCall", "GenoCall", "mks", "pos", "cm", "mk.type", "phase") - all_maps <- fix_genocall_names(all_maps) - saveRDS(all_maps, "data2_maps.rds") - - all_times <- fread("all_times.txt") - colnames(all_times) <- c("SNPCall", "CountsFrom", "GenoCall", "time") - all_times <- fix_genocall_names(all_times) - saveRDS(all_times, "data4_times.rds") - - system("mkdir EmpiricalReads_results") - system("mv gusmap_RDatas.RData sequences_emp.llo data1_depths_geno_prob.rds data2_maps.rds data3_filters.rds data4.rds data4_times.rds names.rds EmpiricalReads_results") - system("tar -czvf EmpiricalReads_results.tar.gz EmpiricalReads_results") - -RSCRIPT` -[INFO] [08/08/2020 23:33:20.343] [cromwell-system-akka.dispatchers.backend-dispatcher-137] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.JointReports:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.JointReports:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.JointReports:NA:1]: executing: # make sure there is no preexisting Docker CID file -rm -f /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/docker_cid -# run as in the original configuration without --rm flag (will remove later) -docker run \ - --cidfile /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/docker_cid \ - -i \ - \ - --entrypoint /bin/bash \ - -v /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports:/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports:delegated \ - cristaniguti/onemap_workflows@sha256:f472f5f2ec0c2176c048ad0406faabf46c1fd3f0246af3c9a732d111b64937d5 /cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/script - -# get the return code (working even if the container was detached) -rc=$(docker wait `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/docker_cid`) - -# remove the container after waiting -docker rm `cat /home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/docker_cid` - -# return exit code -exit $rc -[INFO] [08/08/2020 23:33:23.073] [cromwell-system-akka.dispatchers.backend-dispatcher-138] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.JointReports:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.JointReports:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.JointReports:NA:1]: job id: 23635 -[INFO] [08/08/2020 23:33:23.074] [cromwell-system-akka.dispatchers.backend-dispatcher-138] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.JointReports:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.JointReports:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.JointReports:NA:1]: Status change from - to WaitingForReturnCode -[INFO] [08/08/2020 23:33:24.501] [cromwell-system-akka.dispatchers.backend-dispatcher-137] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-EngineJobExecutionActor-Maps.JointReports:NA:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-BackendJobExecutionActor-Maps.JointReports:NA:1/BackgroundConfigAsyncJobExecutionActor] BackgroundConfigAsyncJobExecutionActor [UUID(ab3ced81)Maps.JointReports:NA:1]: Status change from WaitingForReturnCode to Done -[INFO] [08/08/2020 23:33:28.591] [cromwell-system-akka.dispatchers.engine-dispatcher-6] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f/1408f921-6c91-4dd0-8e32-1871e6da741f-SubWorkflowExecutionActor-SubWorkflow-Maps:-1:1/ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1] ab3ced81-bc04-4d5e-83fc-e756e0794e39-SubWorkflowActor-SubWorkflow-Maps:-1:1 [UUID(ab3ced81)]: Workflow Maps complete. Final Outputs: -{ - "Maps.EmpiricalReads_results": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/EmpiricalReads_results.tar.gz" -} -[INFO] [08/08/2020 23:33:30.631] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f/WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f] WorkflowExecutionActor-1408f921-6c91-4dd0-8e32-1871e6da741f [UUID(1408f921)]: Workflow EmpiricalReads complete. Final Outputs: -{ - "EmpiricalReads.gatk_vcf_multi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi.recode.vcf.gz", - "EmpiricalReads.EmpiricalReads_results": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/EmpiricalReads_results.tar.gz", - "EmpiricalReads.gatk_vcf_bi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi.recode.vcf.gz", - "EmpiricalReads.freebayes_vcf_multi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi.recode.vcf.gz", - "EmpiricalReads.freebayes_vcf_bi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi.recode.vcf.gz" -} -[INFO] [08/08/2020 23:33:30.651] [cromwell-system-akka.dispatchers.engine-dispatcher-58] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor] WorkflowManagerActor WorkflowActor-1408f921-6c91-4dd0-8e32-1871e6da741f is in a terminal state: WorkflowSucceededState -[INFO] [08/08/2020 23:34:22.433] [cromwell-system-akka.dispatchers.engine-dispatcher-27] [akka://cromwell-system/user/SingleWorkflowRunnerActor] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'. -{ - "outputs": { - "EmpiricalReads.gatk_vcf_multi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_multi.recode.vcf.gz", - "EmpiricalReads.EmpiricalReads_results": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-Maps/Maps/ab3ced81-bc04-4d5e-83fc-e756e0794e39/call-JointReports/execution/EmpiricalReads_results.tar.gz", - "EmpiricalReads.gatk_vcf_bi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-GatkGenotyping/GatkGenotyping/73173054-1ece-47fc-9219-1aeee1913879/call-SplitFiltVCF/SplitFiltVCF/1880a9f4-eb6f-4372-8b8b-e190be5b3ac0/call-SplitFilters/execution/gatk_bi.recode.vcf.gz", - "EmpiricalReads.freebayes_vcf_multi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_multi.recode.vcf.gz", - "EmpiricalReads.freebayes_vcf_bi": "/home/cristiane/github/errors_workflow/cromwell-executions/EmpiricalReads/1408f921-6c91-4dd0-8e32-1871e6da741f/call-SNPCalling/SNPCalling/33dd1747-4d8c-454c-b25e-88e026690ad6/call-FreebayesGenotyping/FreebayesGenotyping/7de96f78-bdf6-425c-83c1-cff22fdd180a/call-SplitFiltVCF/SplitFiltVCF/7fafa422-034b-4c9a-9d9f-3dbb290e22d7/call-SplitFilters/execution/freebayes_bi.recode.vcf.gz" - }, - "id": "1408f921-6c91-4dd0-8e32-1871e6da741f" -} -[2020-08-08 23:34:27,12] [info] Workflow polling stopped -[2020-08-08 23:34:27,12] [info] 0 workflows released by cromid-d100dd9 -[2020-08-08 23:34:27,12] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds -[2020-08-08 23:34:27,12] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds -[INFO] [08/08/2020 23:34:27.128] [cromwell-system-akka.dispatchers.engine-dispatcher-62] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor] Aborting all running workflows. -[INFO] [08/08/2020 23:34:27.129] [cromwell-system-akka.actor.default-dispatcher-142] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor] Message [cromwell.engine.workflow.workflowstore.WorkflowStoreActor$WorkDone$] from Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor#633944180] to Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor#633944180] was not delivered. [1] dead letters encountered. If this is not an expected behavior, then [Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowStoreActor/WorkflowStoreEngineActor#633944180]] may have terminated unexpectedly, This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'. -[2020-08-08 23:34:27,12] [info] WorkflowStoreActor stopped -[2020-08-08 23:34:27,13] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds -[2020-08-08 23:34:27,13] [info] JobExecutionTokenDispenser stopped -[2020-08-08 23:34:27,13] [info] WorkflowLogCopyRouter stopped -[2020-08-08 23:34:27,28] [info] Connection pools shut down -[2020-08-08 23:34:27,29] [info] Database closed -[2020-08-08 23:34:27,29] [info] Stream materializer shut down -[2020-08-08 23:34:27,29] [info] WDL HTTP import resolver closed -[2020-08-08 23:34:27,30] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds -[WARN] [08/08/2020 23:34:27.305] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopWorkflowManagerActor] failed in phase [abort-all-workflows]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopSubWorkflowStoreActor] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down JobStoreActor - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopJobStoreActor] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopCallCacheWriteActor] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopServiceRegistryActor] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down DockerHashActor - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopDockerHashActor] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown -[2020-08-08 23:34:27,30] [info] Shutting down IoProxy - Timeout = 1800 seconds -[WARN] [08/08/2020 23:34:27.306] [cromwell-system-akka.actor.default-dispatcher-3] [CoordinatedShutdown(akka://cromwell-system)] Task [stopIoProxy] failed in phase [stop-io-activity]: cannot enqueue after timer shutdown diff --git a/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data1_depths_geno_prob.tsv.gz b/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data1_depths_geno_prob.tsv.gz deleted file mode 100644 index 624db0f..0000000 Binary files a/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data1_depths_geno_prob.tsv.gz and /dev/null differ diff --git a/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data2_maps.tsv.gz b/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data2_maps.tsv.gz deleted file mode 100644 index b254b2e..0000000 Binary files a/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data2_maps.tsv.gz and /dev/null differ diff --git a/inst/ext/toy_sample_emp/diploid/EmpiricalReads_results/data3_filters.tsv.gz 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/dev/null +++ b/man/prepare_poly_datas_emp.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/graphics_poly_emp.R +\name{prepare_poly_datas_emp} +\alias{prepare_poly_datas_emp} +\title{Read empirical input polyploid data} +\usage{ +prepare_poly_datas_emp(x = NULL, example_emp = NULL) +} +\arguments{ +\item{x}{inputted dataset} + +\item{example_emp}{selected example id} +} +\description{ +Read empirical input polyploid data +}