You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am currently working on rampart. I already installed all the dependencies. After that, i tried a test run on ecoli sample data and it already failed with mecq stage
Here is the command:
This is were the error starts:
`
2019-09-24 00:50:53 DEBUG ProcessRunner:153 - Return code was '0' for [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Redirecting stderr.
2019-09-24 00:50:53 DEBUG DefaultProcessService:162 - Finished executing command [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Output:
2019-09-24 00:50:53 ERROR Mecq:181 - MECQ job "quake" for sample "rampart_out" did not produce the expected output file: /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_1.cor.fastq
2019-09-24 00:50:53 ERROR AbstractConanTask:255 - Process 'MECQ' failed to execute, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:257 - Execution exception follows
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:187)
at uk.ac.ebi.fgpt.conan.core.process.AbstractConanProcess.execute(AbstractConanProcess.java:298)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:233)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
at uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
at uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
at uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)
Caused by: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:158)
... 6 more
2019-09-24 00:50:53 DEBUG AbstractConanTask:258 - Is this event to abort: false Output: [Ljava.lang.String;@48f278eb
2019-09-24 00:50:53 ERROR AbstractConanTask:550 - Task 'RAMPART' failed its current process, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:556 - Output follows...
No output captured
2019-09-24 00:50:53 INFO AbstractConanTask:288 - Task 'RAMPART' execution ended. Runtime: 0:00:00.043
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:267)
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)
`
The text was updated successfully, but these errors were encountered:
quake V0.3
kat 1.69
jellyfish 2.3.0
I am currently working on rampart. I already installed all the dependencies. After that, i tried a test run on ecoli sample data and it already failed with mecq stage
Here is the command:
(base) hydra@Biohazard:~/Desktop/5_30_19-Try_rampart/190613$ rampart -v ecoli_full_job.xml
This is were the error starts:
`
2019-09-24 00:50:53 DEBUG ProcessRunner:153 - Return code was '0' for [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Redirecting stderr.
2019-09-24 00:50:53 DEBUG DefaultProcessService:162 - Finished executing command [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Output:
2019-09-24 00:50:53 ERROR Mecq:181 - MECQ job "quake" for sample "rampart_out" did not produce the expected output file: /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_1.cor.fastq
2019-09-24 00:50:53 ERROR AbstractConanTask:255 - Process 'MECQ' failed to execute, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:257 - Execution exception follows
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:187)
at uk.ac.ebi.fgpt.conan.core.process.AbstractConanProcess.execute(AbstractConanProcess.java:298)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:233)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
at uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
at uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
at uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)
Caused by: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:158)
... 6 more
2019-09-24 00:50:53 DEBUG AbstractConanTask:258 - Is this event to abort: false Output: [Ljava.lang.String;@48f278eb
2019-09-24 00:50:53 ERROR AbstractConanTask:550 - Task 'RAMPART' failed its current process, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:556 - Output follows...
No output captured
2019-09-24 00:50:53 INFO AbstractConanTask:288 - Task 'RAMPART' execution ended. Runtime: 0:00:00.043
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:267)
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)
`
The text was updated successfully, but these errors were encountered: