[DOCKTESTERS] Amazon account
Denis Yuen
Denis.Yuen at oicr.on.ca
Tue Sep 20 15:11:27 EDT 2016
Hi,
That's really just saying that cwltool was unable to find the output.
Changing the entry will just save the output somewhere else.
The real problem is probably in the section:
----
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<https://webmail.oicr.on.ca/owa/redir.aspx?REF=y1Ttzt8abm9KcHVrCOpAVQxHU5lEjbYX0cTTaZ9z7jTOE4C4h-HTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
[SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25
Command exit code: 1
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<https://webmail.oicr.on.ca/owa/redir.aspx?REF=84q3BASSDZDe2S4nuestIXsNVwoV_SSc5c4KdmGWDLgodoK4h-HTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
----
That says that pindel failed, but there doesn't appear to be any more explanation as to why.
Denis Yuen
Bioinformatics Software Developer
Ontario Institute for Cancer Research
MaRS Centre
661 University Avenue
Suite 510
Toronto, Ontario, Canada M5G 0A3
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________________________________
From: Miguel Vazquez [mikisvaz at gmail.com]
Sent: September 20, 2016 2:55 PM
To: Junjun Zhang
Cc: Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org
Subject: Re: [DOCKTESTERS] Amazon account
Just a heads up, the process failed.
The complete log is bellow, but I think this is the culprit:
Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']'
I wrote something like this in Dockerstore.json
"somatic_cnv_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz",
"class": "File"
}
I've replace those entries with this
"somatic_cnv_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/DONOR.somatic.cnv.tar.gz",
"class": "File"
}
so that the glob work. I'm trying again. I'll update the documentation
Best
Miguel
------------------
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stderr
-----------------------------------------------------------------------
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_54
Job ID: 335639174
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.e335639174
Updated: Tue Sep 20 03:55:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_13
Job ID: 335639178
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.e335639178
Updated: Tue Sep 20 12:07:55 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_13.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_17
Job ID: 335639179
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.e335639179
Updated: Tue Sep 20 12:05:07 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_15
Job ID: 335639180
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.e335639180
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_48
Job ID: 335639020
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.e335639020
Updated: Tue Sep 20 05:54:57 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_50
Job ID: 335639025
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.e335639025
Updated: Tue Sep 20 04:48:39 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_52
Job ID: 335639111
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.e335639111
Updated: Tue Sep 20 05:05:25 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_56
Job ID: 335639173
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.e335639173
Updated: Tue Sep 20 03:39:33 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.sh
Command exit code: 0
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_38
Job ID: 335638783
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.e335638783
Updated: Tue Sep 20 06:49:18 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_42
Job ID: 335638805
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.e335638805
Updated: Tue Sep 20 06:07:49 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_46
Job ID: 335638826
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.e335638826
Updated: Tue Sep 20 05:40:42 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stderr
-----------------------------------------------------------------------
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_22
Job ID: 335638775
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.e335638775
Updated: Tue Sep 20 09:32:19 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_22.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_28
Job ID: 335638776
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.e335638776
Updated: Tue Sep 20 08:57:31 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_28.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_32
Job ID: 335638777
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.e335638777
Updated: Tue Sep 20 08:12:44 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_32.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_34
Job ID: 335638778
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.e335638778
Updated: Tue Sep 20 08:24:35 UTC 2016
Job Name: s58_unpackRef_NA_9
Job ID: 331891142
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.e331891142
Updated: Tue Sep 20 00:39:16 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_9.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_verifyBamHomChk_control_6
Job ID: 331891143
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.e331891143
Updated: Tue Sep 20 00:44:52 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_verifyBamHomChk_control_6.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_basFileGenerate_control_11
Job ID: 332292910
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.e332292910
Updated: Tue Sep 20 01:20:39 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_basFileGenerate_control_11.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_unpackRef_NA_10
Job ID: 332292911
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.e332292911
Updated: Tue Sep 20 00:44:57 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_unpackRef_NA_10.sh
Command exit code: 0
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_mark_start_1
Job ID: 331890603
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.e331890603
Updated: Tue Sep 20 00:38:10 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_mark_start_1.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_prepBam_control_3
Job ID: 331890831
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.e331890831
Updated: Tue Sep 20 00:38:11 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_control_3.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_prepBam_tumour_2
Job ID: 331890832
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.e331890832
Updated: Tue Sep 20 00:38:11 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_prepBam_tumour_2.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_BRASS_input_99
Job ID: 379374477
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.o379374477
Updated: Tue Sep 20 16:49:15 UTC 2016
Contents Excerpt:
[V] 18 0.49745MB/s 1781.56
[V] 19 0.525041MB/s 1879.07
[V] 20 0.552722MB/s 1976.44
[V] 21 0.579942MB/s 2072.21
[V] 22 0.607543MB/s 2169.2
[V] 23 0.635118MB/s 2266.04
[V] 24264262
[V] MemUsage(size=71.1484,rss=10.9336,peak=291.977) wall clock time 02:57:24:31175299
11827.06user 310.09system 2:59:40elapsed 112%CPU (0avgtext+0avgdata 4265632maxresident)k
117507424inputs+14421104outputs (84major+234838minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_BRASS_input_99.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.o379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
87.14user 5.10system 1:41.25elapsed 91%CPU (0avgtext+0avgdata 66448maxresident)k
2720952inputs+4360560outputs (5major+7600minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stdout
-----------------------------------------------------------------------
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 54.9M 100 54.9M 0 0 1016k 0 0:00:55 0:00:55 --:--:-- 1047k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 174k 100 174k 0 0 174k 0 0:00:01 0:00:01 --:--:-- 567k
[2016/09/20 16:49:15] | Output for stderr due to workflow run failure:
-----------------------------------------------------------------------
Job Name: s58_start_0
Job ID: 331890362
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_start_0.e331890362
Updated: Tue Sep 20 00:38:10 UTC 2016
Contents Excerpt:
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.o373317274
Updated: Tue Sep 20 12:08:37 UTC 2016
Contents Excerpt:
Modified command: cp /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-44fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_renameSampleFile_208.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_57
Job ID: 373317275
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.o373317275
Updated: Tue Sep 20 13:29:27 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.23.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
4798.51user 50.73system 1:20:50elapsed 99%CPU (0avgtext+0avgdata 3115856maxresident)k
9833328inputs+56328outputs (0major+199552minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_57.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_60
Job ID: 379374473
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.o379374473
Updated: Tue Sep 20 15:34:45 UTC 2016
Contents Excerpt:
Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
5928.09user 101.55system 1:45:10elapsed 95%CPU (0avgtext+0avgdata 2345888maxresident)k
221140208inputs+43144outputs (37major+169349minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_61
Job ID: 379374475
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.o379374475
Updated: Tue Sep 20 14:58:41 UTC 2016
Contents Excerpt:
Errors from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
3864.82user 67.24system 1:09:07elapsed 94%CPU (0avgtext+0avgdata 2350544maxresident)k
157460240inputs+43120outputs (57major+167795minor)pagefaults 0swaps
11476.37user 140.61system 6:48:23elapsed 47%CPU (0avgtext+0avgdata 3035728maxresident)k
7380072inputs+56816outputs (0major+196640minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_41
Job ID: 335639489
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.o335639489
Updated: Tue Sep 20 07:35:04 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.15.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
9429.90user 117.09system 5:54:22elapsed 44%CPU (0avgtext+0avgdata 2739152maxresident)k
5273744inputs+51000outputs (0major+177355minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_41.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_45
Job ID: 335639845
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.o335639845
Updated: Tue Sep 20 07:29:41 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.17.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
9231.30user 116.04system 5:49:00elapsed 44%CPU (0avgtext+0avgdata 2540400maxresident)k
5255296inputs+46736outputs (0major+165277minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_45.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_43
Job ID: 335639853
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.o335639853
Updated: Tue Sep 20 08:28:45 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr16.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.16.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
11465.31user 146.48system 6:48:03elapsed 47%CPU (0avgtext+0avgdata 2945712maxresident)k
6906080inputs+54432outputs (0major+190932minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_43.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_renameSampleFile_208
Job ID: 373317274
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_33
Job ID: 335639420
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.o335639420
Updated: Tue Sep 20 10:42:41 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr11.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.11.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
18904.62user 233.41system 9:02:00elapsed 58%CPU (0avgtext+0avgdata 4537600maxresident)k
15888800inputs+86400outputs (0major+292553minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_33.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_35
Job ID: 335639430
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.o335639430
Updated: Tue Sep 20 10:03:48 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr12.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.12.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
16584.76user 210.26system 8:23:07elapsed 55%CPU (0avgtext+0avgdata 4373600maxresident)k
12917040inputs+82896outputs (0major+281480minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_35.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_37
Job ID: 335639431
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.o335639431
Updated: Tue Sep 20 08:26:17 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.13.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
11361.18user 138.30system 6:45:36elapsed 47%CPU (0avgtext+0avgdata 3301008maxresident)k
7418080inputs+62192outputs (0major+212951minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_37.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_39
Job ID: 335639452
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_39.o335639452
Updated: Tue Sep 20 08:29:04 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr14.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.14.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
Updated: Tue Sep 20 11:02:29 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr7.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.7.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20088.69user 242.69system 9:21:48elapsed 60%CPU (0avgtext+0avgdata 5281504maxresident)k
18604808inputs+96776outputs (0major+339332minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_27
Job ID: 335639400
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.o335639400
Updated: Tue Sep 20 11:02:53 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr8.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.8.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20108.48user 243.42system 9:22:11elapsed 60%CPU (0avgtext+0avgdata 5228912maxresident)k
17295080inputs+95440outputs (0major+335764minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_27.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_29
Job ID: 335639401
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.o335639401
Updated: Tue Sep 20 09:18:32 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr9.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.9.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
13962.23user 175.03system 7:37:51elapsed 51%CPU (0avgtext+0avgdata 3971872maxresident)k
12246072inputs+72144outputs (0major+255173minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_29.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_31
Job ID: 335639417
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.o335639417
Updated: Tue Sep 20 10:11:08 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr10.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.10.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
17052.42user 207.86system 8:30:26elapsed 56%CPU (0avgtext+0avgdata 4504144maxresident)k
13931760inputs+85488outputs (0major+289717minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_31.stdout
-----------------------------------------------------------------------
23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_15
Job ID: 335639180
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.o335639180
Updated: Tue Sep 20 12:08:37 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr2.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.2.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
24021.20user 275.32system 10:27:56elapsed 64%CPU (0avgtext+0avgdata 7851136maxresident)k
24358016inputs+146264outputs (0major+499924minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_15.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_19
Job ID: 335639200
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.o335639200
Updated: Tue Sep 20 11:57:43 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr4.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.4.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
23336.68user 273.00system 10:17:02elapsed 63%CPU (0avgtext+0avgdata 6501344maxresident)k
22397816inputs+120192outputs (0major+416448minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_19.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_23
Job ID: 335639375
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.o335639375
Updated: Tue Sep 20 11:14:37 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr6.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.6.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
20846.11user 251.83system 9:33:55elapsed 61%CPU (0avgtext+0avgdata 5765024maxresident)k
19462064inputs+106080outputs (0major+369701minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_23.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_25
Job ID: 335639387
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_25.o335639387
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_56
Job ID: 335639173
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.o335639173
Updated: Tue Sep 20 03:39:33 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr22.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.22.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
2810.79user 34.33system 1:58:52elapsed 39%CPU (0avgtext+0avgdata 1250144maxresident)k
1243552inputs+22208outputs (0major+82726minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_56.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_54
Job ID: 335639174
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.o335639174
Updated: Tue Sep 20 03:55:15 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr21.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.21.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
3187.08user 39.68system 2:14:34elapsed 39%CPU (0avgtext+0avgdata 1302656maxresident)k
1689216inputs+23256outputs (0major+86038minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_54.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_58
Job ID: 335639178
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.o335639178
Updated: Tue Sep 20 04:41:10 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr23.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.23.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4375.73user 53.14system 3:00:29elapsed 40%CPU (0avgtext+0avgdata 3123136maxresident)k
4325272inputs+56240outputs (0major+199643minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_58.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_tumour_17
Job ID: 335639179
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_tumour_17.o335639179
Updated: Tue Sep 20 12:05:07 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr3.txt -o /var/spool/cwl/bbCounts/b02b4bba-6e66-44fb-a48f-38c309aaaac5.3.tsv -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam
23819.53user 283.10system 10:24:27elapsed 64%CPU (0avgtext+0avgdata 6576048maxresident)k
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr17.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.17.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
5945.65user 71.96system 4:00:01elapsed 41%CPU (0avgtext+0avgdata 2544496maxresident)k
5572568inputs+46720outputs (0major+163875minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_46.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_48
Job ID: 335639020
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.o335639020
Updated: Tue Sep 20 05:54:57 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr18.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.18.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
6337.11user 77.66system 4:14:16elapsed 42%CPU (0avgtext+0avgdata 2647504maxresident)k
5337616inputs+48704outputs (0major+170347minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_48.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_50
Job ID: 335639025
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.o335639025
Updated: Tue Sep 20 04:48:39 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr19.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.19.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4542.91user 55.47system 3:07:58elapsed 40%CPU (0avgtext+0avgdata 1995904maxresident)k
3514080inputs+36192outputs (0major+129470minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_50.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_52
Job ID: 335639111
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.o335639111
Updated: Tue Sep 20 05:05:25 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr20.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.20.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
4979.15user 61.39system 3:24:44elapsed 41%CPU (0avgtext+0avgdata 2102832maxresident)k
3653168inputs+38272outputs (0major+136206minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_52.stdout
-----------------------------------------------------------------------
-6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
11287.76user 142.04system 6:43:55elapsed 47%CPU (0avgtext+0avgdata 4543376maxresident)k
9747344inputs+86048outputs (0major+289230minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_34.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_38
Job ID: 335638783
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.o335638783
Updated: Tue Sep 20 06:49:18 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr13.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.13.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
7981.44user 98.27system 5:08:39elapsed 43%CPU (0avgtext+0avgdata 3310512maxresident)k
6948640inputs+62176outputs (7major+211942minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_38.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_42
Job ID: 335638805
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.o335638805
Updated: Tue Sep 20 06:07:49 UTC 2016
Contents Excerpt:
Modified command: alleleCounter -l /var/spool/cwl/reference_files/battenberg/1000genomesloci/1000genomesloci2012_chr15.txt -o /var/spool/cwl/bbCounts/8c0354eb-6a3e-4a98-b41c-f8add599884c.15.tsv -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam
6705.59user 83.09system 4:27:09elapsed 42%CPU (0avgtext+0avgdata 2746816maxresident)k
6146600inputs+50992outputs (0major+176574minor)pagefaults 0swaps
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_control_42.stdout
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_control_46
Job ID: 379374477
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477
Updated: Tue Sep 20 13:50:00 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<redir.aspx?REF=hsSMXKX7Van9j73HyCbJW2nw85pqUjxRPrOv4TAGzMFyj6OMieHTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
[SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25
Command exit code: 1
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<redir.aspx?REF=hsSMXKX7Van9j73HyCbJW2nw85pqUjxRPrOv4TAGzMFyj6OMieHTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15
Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f
f: command not found
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df
Filesystem 1K-blocks Used Available Use% Mounted on
udev 62947280 12 62947268 1% /dev
tmpfs 12590448 364 12590084 1% /run
/dev/xvda1 8115168 6093092 1586800 80% /
none 4 0 4 0% /sys/fs/cgroup
none 5120 0 5120 0% /run/lock
none 62952228 0 62952228 0% /run/shm
none 102400 0 102400 0% /run/user
/dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 61G 12K 61G 1% /dev
tmpfs 13G 364K 13G 1% /run
/dev/xvda1 7.8G 5.9G 1.6G 80% /
none 4.0K 0 4.0K 0% /sys/fs/cgroup
none 5.0M 0 5.0M 0% /run/lock
none 61G 0 61G 0% /run/shm
none 100M 0 100M 0% /run/user
/dev/xvdb 985G 290G 645G 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json
{
"bbFrom": {
"bbFrom": {
"path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_battenberg.tar.gz<redir.aspx?REF=25LACK-NitS8CiBDdhQTNUEDJ0rw5dBaGIlyFnfupW5yj6OMieHTCAFodHRwczovL3MzLWV1LXdlc3QtMS5hbWF6b25hd3MuY29tL3d0c2ktcGFuY2FuY2VyL3JlZmVyZW5jZS9HUkNoMzdkNV9iYXR0ZW5iZXJnLnRhci5neg..>",
"class": "File"
},
"refFrom": {
"path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference/GRCh37d5_CGP_refBundle.tar.gz<redir.aspx?REF=SYSPizPfvDY-BEbyrZ8Ga7lU3tz9WfYttsX20QlhIXVyj6OMieHTCAFodHRwczovL3MzLWV1LXdlc3QtMS5hbWF6b25hd3MuY29tL3d0c2ktcGFuY2FuY2VyL3JlZmVyZW5jZS9HUkNoMzdkNV9DR1BfcmVmQnVuZGxlLnRhci5neg..>",
"class": "File"
},
"tumor": {
"path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99bf370aada0.bam",
"class": "File"
},
"normal": {
"path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca9566c58e0.bam",
"class": "File"
},
"somatic_sv_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.sv.tar.gz",
"class": "File"
},
"somatic_snv_mnv_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.snv.mnv.tar.gz",
"class": "File"
},
"somatic_verifyBamId_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.verifyBamId.tar.gz",
"class": "File"
},
"somatic_cnv_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.cnv.tar.gz",
"class": "File"
},
"somatic_imputeCounts_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.imputeCounts.tar.gz",
"class": "File"
},
"somatic_genotype_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genotype.tar.gz",
"class": "File"
},
"somatic_indel_tar_gz": {
"path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.indel.tar.gz",
"class": "File"
}
}
~
~
~
~
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ l results/
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json ^C
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15
Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ f
f: command not found
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df
Filesystem 1K-blocks Used Available Use% Mounted on
udev 62947280 12 62947268 1% /dev
tmpfs 12590448 364 12590084 1% /run
/dev/xvda1 8115168 6093092 1586800 80% /
none 4 0 4 0% /sys/fs/cgroup
none 5120 0 5120 0% /run/lock
none 62952228 0 62952228 0% /run/shm
none 102400 0 102400 0% /run/user
/dev/xvdb 1031992064 303267080 676279800 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 61G 12K 61G 1% /dev
tmpfs 13G 364K 13G 1% /run
/dev/xvda1 7.8G 5.9G 1.6G 80% /
none 4.0K 0 4.0K 0% /sys/fs/cgroup
none 5.0M 0 5.0M 0% /run/lock
none 61G 0 61G 0% /run/shm
none 100M 0 100M 0% /run/user
/dev/xvdb 985G 290G 645G 31% /mnt/1TB
ubuntu at ip-10-24-20-69:~/DockerTest-Miguel/Sanger$ vi Dockstore.json
{
Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/7875b5196f6b8b52847f99bf370aada0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/b02b4bba-6e66-44fb-a48f-38c309aaaac5.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_60.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_ASCAT_allele_count_61
Job ID: 379374475
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.e379374475
Updated: Tue Sep 20 14:58:41 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.sh
Command exit code: 0
Output from command: /opt/wtsi-cgp/bin/alleleCounter -b /var/spool/cwl/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/ascat/tmpAscat/allele_count/8c0354eb-6a3e-4a98-b41c-f8add599884c.allct -l /var/spool/cwl/reference_files/ascat/SnpLocus.tsv -m 20
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_ASCAT_allele_count_61.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_cgpPindel_input_70
Job ID: 379374477
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.e379374477
Updated: Tue Sep 20 13:50:00 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.sh
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<redir.aspx?REF=hsSMXKX7Van9j73HyCbJW2nw85pqUjxRPrOv4TAGzMFyj6OMieHTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
[SeqWare Pipeline] ERROR [2016/09/20 13:50:00] | The exit value was 25
Command exit code: 1
Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl<redir.aspx?REF=hsSMXKX7Van9j73HyCbJW2nw85pqUjxRPrOv4TAGzMFyj6OMieHTCAFodHRwOi8vcGluZGVsX2lucHV0X2dlbi5wbA..> -b /var/lib/cwl/stg33415604-d4eb-49aa-8f81-345b6fb2a6f3/fdcb1bd7cffca69d15383ca9566c58e0.bam -o /var/spool/cwl/0/pindel/tmpPindel/8c0354eb-6a3e-4a98-b41c-f8add599884c -t 4 -e /var/spool/cwl/reference_files/brass/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_cgpPindel_input_70.stderr
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Job Name: s58_bbAllele_merge_59
Job ID: 379374478
File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.e379374478
Updated: Tue Sep 20 13:51:15 UTC 2016
Contents Excerpt:
Command run:
bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.sh
Command exit code: 0
Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/generated-scripts/s58_bbAllele_merge_59.stderr
-----------------------------------------------------------------------
The method 'do_run' exited abnormally so the Runner will terminate here!
Return value was: 15
[WARNING] command: seqware bundle launch --dir /home/seqware/CGP-Somatic-Docker/target/Workflow_Bundle_CgpSomaticCore_0.0.0_SeqWare_1.1.1/ --engine whitestar-parallel --ini /var/spool/cwl/workflow.ini --no-metadata exited with code: 15
Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']'
[job temp319312608049643386.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/outputs/ --tmpdir-prefix /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/working/ /tmp/1474331255066-0/temp319312608049643386.cwl /mnt/1TB/work/DockerTest-Miguel/Sanger/./datastore/launcher-780ac637-b999-4a70-8ab7-79b51c64f428/workflow_params.json
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