-
Notifications
You must be signed in to change notification settings - Fork 12
example output
snamburi3 edited this page Mar 7, 2017
·
2 revisions
ubuntu@ip-172-31-20-25:/mnt/data/cloudneo$ ~/rabix-backend-local-1.0.0-rc3/rabix cloudneo.cwl inputs.json
[2017-03-07 18:04:23.529] [INFO] Pulling docker image samtools:cloudneo
[2017-03-07 18:04:23.539] [INFO] Pulling docker image variant-effect-predictor:cloudneo
[2017-03-07 18:04:24.282] [INFO] Running command line: samtools fastq /mnt/data/cloudneo/sample.bam > sample.fastq
[2017-03-07 18:04:24.373] [INFO] Running command line: tar xfz /mnt/data/cloudneo/homo_sapiens_vep_83_GRCh37.tar.gz -C /opt/variant_effect_predictor_83/cache && perl /opt/variant_effect_predictor_83/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl --input_file /mnt/data/cloudneo/sample.vcf --dir /opt/variant_effect_predictor_83/cache --offline --output_file sample.vep.vcf --stats_file sample.vep.vcf_summary.html --filter_common --html --vcf
[2017-03-07 18:04:24.573] [INFO] Job root.samtools_fastq has started
[2017-03-07 18:04:24.831] [INFO] Job root.Variant_Effect_Predictor has started
[2017-03-07 18:05:51.127] [INFO] Job root.samtools_fastq has completed
[2017-03-07 18:05:51.330] [INFO] Pulling docker image bwa:cloudneo
[2017-03-07 18:05:51.358] [INFO] Running command line: bwa aln -e 0 -o 0 /mnt/data/cloudneo/HLA-I_II_CDS.fasta /mnt/data/cloudneo/cloudneo-20170307180422264/root/samtools_fastq/sample.fastq > sample.aln.sai
[2017-03-07 18:05:51.582] [INFO] Job root.bwa_aln has started
[2017-03-07 18:09:39.329] [INFO] Job root.bwa_aln has completed
[2017-03-07 18:09:39.429] [INFO] Pulling docker image bwa:cloudneo
[2017-03-07 18:09:39.467] [INFO] Running command line: bwa samse /mnt/data/cloudneo/HLA-I_II_CDS.fasta /mnt/data/cloudneo/cloudneo-20170307180422264/root/bwa_aln/sample.aln.sai /mnt/data/cloudneo/cloudneo-20170307180422264/root/samtools_fastq/sample.fastq > sample.sam
[2017-03-07 18:09:39.723] [INFO] Job root.bwa_sampe has started
[2017-03-07 18:11:33.157] [INFO] Job root.bwa_sampe has completed
[2017-03-07 18:11:33.228] [INFO] Pulling docker image hlaminer:cloudneo
[2017-03-07 18:11:33.248] [INFO] Running command line: /usr/local/bin/HLAminer_v1.3/bin/HLAminer.pl -a /mnt/data/cloudneo/cloudneo-20170307180422264/root/bwa_sampe/sample.sam -s 500 -h /mnt/data/cloudneo/HLA-I_II_CDS.fasta -e 1
[2017-03-07 18:11:33.482] [INFO] Job root.hlaminer has started
[2017-03-07 18:13:23.139] [INFO] Job root.hlaminer has completed
[2017-03-07 18:15:15.347] [INFO] Job root.Variant_Effect_Predictor has completed
[2017-03-07 18:15:15.429] [INFO] Pulling docker image python:2.7
[2017-03-07 18:15:15.452] [INFO] Running command line: python add_header.py /mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf > sample.vep.nochr.vcf
[2017-03-07 18:15:15.673] [INFO] Job root.vcf_parser has started
[2017-03-07 18:15:17.166] [INFO] Job root.vcf_parser has completed
[2017-03-07 18:15:17.333] [INFO] Pulling docker image protein-translator:cloudneo
[2017-03-07 18:15:17.364] [INFO] Running command line: Rscript protein_translator.r /mnt/data/cloudneo/Homo_sapiens.GRCh37.75.gtf /mnt/data/cloudneo/HumanProteins.GRCh37.75.csv /mnt/data/cloudneo/cloudneo-20170307180422264/root/vcf_parser/sample.vep.nochr.vcf sample.vep.exome.xls sample.vep.normal.fasta sample.vep.tumor.fasta 10
[2017-03-07 18:15:17.581] [INFO] Job root.Protein_Translator has started
[2017-03-07 18:16:00.082] [INFO] Job root.Protein_Translator has completed
[2017-03-07 18:16:00.230] [INFO] Pulling docker image netmhcpan:cloudneo
[2017-03-07 18:16:00.231] [INFO] Pulling docker image netmhcpan:cloudneo
[2017-03-07 18:16:00.252] [INFO] Running command line: python netmhcpan_parser.py -f /mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.tumor.fasta -hla /mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv -d /mnt/data/cloudneo/netmhcpan-3.0.imgt.fasta -l 9 && mv outputs/* .
[2017-03-07 18:16:00.270] [INFO] Running command line: python netmhcpan_parser.py -f /mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.normal.fasta -hla /mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv -d /mnt/data/cloudneo/netmhcpan-3.0.imgt.fasta -l 9 && mv outputs/* .
[2017-03-07 18:16:00.578] [INFO] Job root.netmhcpan has started
[2017-03-07 18:16:00.727] [INFO] Job root.netmhcpan_1 has started
[2017-03-07 18:23:04.175] [INFO] Job root.netmhcpan has completed
[2017-03-07 18:23:04.185] [INFO] Job root.netmhcpan_1 has completed
{
"control_fasta_1" : {
"checksum" : "sha1$b57bde2e853cf6ea704fb80767ee726212111934",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.normal.fasta",
"name" : "sample.vep.normal.fasta",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.normal.fasta",
"secondaryFiles" : [ ],
"size" : 3330
},
"html_output" : {
"checksum" : "sha1$91dd6e9e1ca7119c7f8ca013b7a0bbf8c5440cff",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf.html",
"name" : "sample.vep.vcf.html",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf.html",
"secondaryFiles" : [ ],
"size" : 16414
},
"html_summary" : {
"checksum" : "sha1$9b1a0d38e468803a15427a56c299e500cc8516b3",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf_summary.html",
"name" : "sample.vep.vcf_summary.html",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf_summary.html",
"secondaryFiles" : [ ],
"size" : 16520
},
"netmhcpan_outputs_txt" : [ {
"checksum" : "sha1$c59a83f49e21f36df0f13fcf1bf165c2621d7fb9",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A23-01.txt",
"name" : "sample.vep.tumor.HLA-A23-01.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A23-01.txt",
"secondaryFiles" : [ ],
"size" : 249859
}, {
"checksum" : "sha1$741cf87b1e1d4a0f9bfe83feec858ed0fcc1b4bb",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A24-02.txt",
"name" : "sample.vep.tumor.HLA-A24-02.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A24-02.txt",
"secondaryFiles" : [ ],
"size" : 249913
}, {
"checksum" : "sha1$5f481944dac74a261d5e735c373ca7688ef26f38",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B40-06.txt",
"name" : "sample.vep.tumor.HLA-B40-06.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B40-06.txt",
"secondaryFiles" : [ ],
"size" : 249871
}, {
"checksum" : "sha1$8cae5b6eff2757ab9a41bc16bb8c13e7fccf648f",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B53-01.txt",
"name" : "sample.vep.tumor.HLA-B53-01.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B53-01.txt",
"secondaryFiles" : [ ],
"size" : 249985
}, {
"checksum" : "sha1$99c48bcae7395a6c5d04c63f47fc778bfd28a1b8",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-C06-103.txt",
"name" : "sample.vep.tumor.HLA-C06-103.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-C06-103.txt",
"secondaryFiles" : [ ],
"size" : 224720
} ],
"netmhcpan_outputs_txt_2" : [ {
"checksum" : "sha1$21e67ddb3157f54c559fd4ef9a6cb7bbac3cf0db",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B53-01.txt",
"name" : "sample.vep.normal.HLA-B53-01.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B53-01.txt",
"secondaryFiles" : [ ],
"size" : 249933
}, {
"checksum" : "sha1$6a5952309473045182b93a8150fd755d99e23282",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-C06-103.txt",
"name" : "sample.vep.normal.HLA-C06-103.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-C06-103.txt",
"secondaryFiles" : [ ],
"size" : 224728
}, {
"checksum" : "sha1$d230e347dd14edfcab76008999dfd946db44cb8c",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A23-01.txt",
"name" : "sample.vep.normal.HLA-A23-01.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A23-01.txt",
"secondaryFiles" : [ ],
"size" : 249843
}, {
"checksum" : "sha1$d271e7629900262d48350f9f757542e482e06248",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A24-02.txt",
"name" : "sample.vep.normal.HLA-A24-02.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A24-02.txt",
"secondaryFiles" : [ ],
"size" : 249879
}, {
"checksum" : "sha1$3ff6edb83704b58df11e0f703338f666327a644e",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B40-06.txt",
"name" : "sample.vep.normal.HLA-B40-06.txt",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B40-06.txt",
"secondaryFiles" : [ ],
"size" : 249837
} ],
"netmhcpan_outputs_xls" : [ {
"checksum" : "sha1$243328f863522afd51e837b8bead949b88544aca",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A24-02.xls",
"name" : "sample.vep.tumor.HLA-A24-02.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A24-02.xls",
"secondaryFiles" : [ ],
"size" : 101002
}, {
"checksum" : "sha1$ee962f6ad3be2035b6b3b97827446e8d69a56b49",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A23-01.xls",
"name" : "sample.vep.tumor.HLA-A23-01.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-A23-01.xls",
"secondaryFiles" : [ ],
"size" : 100971
}, {
"checksum" : "sha1$61e1cea00a1945f0d70fa8feac1581308f9f6e4b",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B40-06.xls",
"name" : "sample.vep.tumor.HLA-B40-06.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B40-06.xls",
"secondaryFiles" : [ ],
"size" : 101140
}, {
"checksum" : "sha1$e61897b9707be38e3edd1e46514a0eacf2a1567f",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-C06-103.xls",
"name" : "sample.vep.tumor.HLA-C06-103.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-C06-103.xls",
"secondaryFiles" : [ ],
"size" : 102602
}, {
"checksum" : "sha1$17f0fb4a396d8c34c5b5bb8274da6464d118b6f6",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B53-01.xls",
"name" : "sample.vep.tumor.HLA-B53-01.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan/sample.vep.tumor.HLA-B53-01.xls",
"secondaryFiles" : [ ],
"size" : 100963
} ],
"netmhcpan_outputs_xls_2" : [ {
"checksum" : "sha1$519ea01a71c912c99f6bf14816fe4f746edaabf2",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B53-01.xls",
"name" : "sample.vep.normal.HLA-B53-01.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B53-01.xls",
"secondaryFiles" : [ ],
"size" : 100985
}, {
"checksum" : "sha1$0904c1128fa344befef05d8aeed48ca9ee64df94",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A24-02.xls",
"name" : "sample.vep.normal.HLA-A24-02.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A24-02.xls",
"secondaryFiles" : [ ],
"size" : 101067
}, {
"checksum" : "sha1$2db470956d8a8961260f546cecd2d13a5c33cdf7",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-C06-103.xls",
"name" : "sample.vep.normal.HLA-C06-103.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-C06-103.xls",
"secondaryFiles" : [ ],
"size" : 102633
}, {
"checksum" : "sha1$44c65bba242ecea3b9691cedfe7e1c782fbba4aa",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A23-01.xls",
"name" : "sample.vep.normal.HLA-A23-01.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-A23-01.xls",
"secondaryFiles" : [ ],
"size" : 101022
}, {
"checksum" : "sha1$8685a04dcde27e554b9d401d8b9eaae67dae28b8",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B40-06.xls",
"name" : "sample.vep.normal.HLA-B40-06.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/netmhcpan_1/sample.vep.normal.HLA-B40-06.xls",
"secondaryFiles" : [ ],
"size" : 101158
} ],
"output_vcf_file" : {
"checksum" : "sha1$fd2b26c0bcad12d36b3306df9d1f33f29b474936",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/vcf_parser/sample.vep.nochr.vcf",
"name" : "sample.vep.nochr.vcf",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/vcf_parser/sample.vep.nochr.vcf",
"secondaryFiles" : [ ],
"size" : 115214
},
"output_xls" : {
"checksum" : "sha1$026de8872196090857b01ae29a5139f19588a4cf",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.exome.xls",
"name" : "sample.vep.exome.xls",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.exome.xls",
"secondaryFiles" : [ ],
"size" : 132611
},
"predictions_file" : {
"checksum" : "sha1$337c7335490c991715215ad22b3093c2004e7ed7",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv",
"name" : "HLAminer_HPRA.csv",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv",
"secondaryFiles" : [ ],
"size" : 2971
},
"tumor_fasta_1" : {
"checksum" : "sha1$ee8f5c634c3c0f4e16a54b18e45c21e2607aa891",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.tumor.fasta",
"name" : "sample.vep.tumor.fasta",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.tumor.fasta",
"secondaryFiles" : [ ],
"size" : 3330
},
"vep_output" : {
"checksum" : "sha1$033b53ff21de5e550a944f5235a0666f3f404078",
"class" : "File",
"location" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf",
"metadata" : { },
"name" : "sample.vep.vcf",
"path" : "/mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf",
"secondaryFiles" : [ ],
"size" : 5766859
}
}