[DOCKTESTERS] Amazon account
Miguel Vazquez
mikisvaz at gmail.com
Tue Sep 20 15:15:28 EDT 2016
Well, that's a bummer. Any ideas?
On Sep 20, 2016 9:11 PM, "Denis Yuen" <Denis.Yuen at oicr.on.ca> wrote:
> 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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> *www.oicr.on.ca <http://www.oicr.on.ca/>*
>
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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
> <http://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
> <http://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
> <http://redir.aspx?REF=25LACK-NitS8CiBDdhQTNUEDJ0rw5dBaGIlyFnfupW5yj6OMieHTCAFodHRwczovL3MzLWV1LXdlc3QtMS5hbWF6b25hd3MuY29tL3d0c2ktcGFuY2FuY2VyL3JlZmVyZW5jZS9HUkNoMzdkNV9iYXR0ZW5iZXJnLnRhci5neg..>
> ",
> "class": "File"
> },
> "refFrom": {
> "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/
> reference/GRCh37d5_CGP_refBundle.tar.gz
> <http://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
> <http://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
> <http://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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