[DOCKTESTERS] Amazon account
Miguel Vazquez
miguel.vazquez at cnio.es
Wed Sep 21 11:13:03 EDT 2016
Thanks Denis, I will try it as soon as I have a change and get back to you
On Wed, Sep 21, 2016 at 4:15 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:
> Hi,
> One additional thought. Before investigating error code 25, try running
> the test data https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/
> blob/develop/test1.json
> This can help us narrow down whether there is an issue with the
> environment or whether there is an issue with the data.
> The test data can be downloaded from the link documented at
> https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker#
> running-with-the-dockstore-command-line
>
> Also a reminder to send the output starting with "docker run -i", this
> will let me see if there's anything obviously strange with the call to
> Docker.
>
> *Denis Yuen*
> Bioinformatics Software Developer
>
>
> *Ontario* *Institute* *for* *Cancer* *Research*
> MaRS Centre
> 661 University Avenue
> Suite 510
> Toronto, Ontario, Canada M5G 0A3
>
> Toll-free: 1-866-678-6427
> Twitter: @OICR_news
> *www.oicr.on.ca <http://www.oicr.on.ca/>*
>
> This message and any attachments may contain confidential and/or
> privileged information for the sole use of the intended recipient. Any
> review or distribution by anyone other than the person for whom it was
> originally intended is strictly prohibited. If you have received this
> message in error, please contact the sender and delete all copies.
> Opinions, conclusions or other information contained in this message may
> not be that of the organization.
> ------------------------------
> *From:* Junjun Zhang
> *Sent:* September 20, 2016 4:09 PM
> *To:* Denis Yuen; Miguel Vazquez
> *Cc:* docktesters at lists.icgc.org; Brian O'Connor
> *Subject:* RE: [DOCKTESTERS] Amazon account
>
> My run failed with same error message.
>
>
> ------------------------------
> *From:* Denis Yuen
> *Sent:* Tuesday, September 20, 2016 3:20 PM
> *To:* Miguel Vazquez
> *Cc:* docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang
> *Subject:* RE: [DOCKTESTERS] Amazon account
>
> I think there are a few pieces of information that could be useful.
>
> Look in this ticket https://github.com/ICGC-TCGA-
> PanCancer/CGP-Somatic-Docker/issues/5 <http://UrlBlockedError.aspx>
> there's a section that starts with "docker run -i", this will let me see if
> there's anything obviously strange with the call to Docker.
>
> Failing that, I think we'll have to see what exit code 25 denotes for
> Pindel.
>
>
> ------------------------------
> *From:* Miguel Vazquez [mikisvaz at gmail.com]
> *Sent:* September 20, 2016 3:15 PM
> *To:* Denis Yuen
> *Cc:* docktesters at lists.icgc.org; Brian O'Connor; Junjun Zhang
> *Subject:* RE: [DOCKTESTERS] Amazon account
>
> Well, that's a bummer. Any ideas?
>
> On Sep 20, 2016 9:11 PM, "Denis Yuen" <Denis.Yuen at oicr.on.ca
> <http://UrlBlockedError.aspx>> 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/genera
>> ted-scripts/s58_cgpPindel_input_70.sh
>>
>> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl
>> <http://UrlBlockedError.aspx> -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_mrg100
>> 0_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://UrlBlockedError.aspx> -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_mrg100
>> 0_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
>>
>> Toll-free: 1-866-678-6427
>> Twitter: @OICR_news
>> *www.oicr.on.ca <http://UrlBlockedError.aspx>*
>>
>> This message and any attachments may contain confidential and/or
>> privileged information for the sole use of the intended recipient. Any
>> review or distribution by anyone other than the person for whom it was
>> originally intended is strictly prohibited. If you have received this
>> message in error, please contact the sender and delete all copies.
>> Opinions, conclusions or other information contained in this message may
>> not be that of the organization.
>> ------------------------------
>> *From:* Miguel Vazquez [mikisvaz at gmail.com <http://UrlBlockedError.aspx>]
>> *Sent:* September 20, 2016 2:55 PM
>> *To:* Junjun Zhang
>> *Cc:* Denis Yuen; Brian O'Connor; docktesters at lists.icgc.org
>> <http://UrlBlockedError.aspx>
>> *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/genera
>> ted-scripts/s58_bbAllele_tumour_25.stderr
>> -----------------------------------------------------------------------
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_56.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_54
>> Job ID: 335639174
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_54.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_54.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_13
>> Job ID: 335639178
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_13.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_tumour_13.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_17
>> Job ID: 335639179
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_17.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_tumour_17.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_15
>> Job ID: 335639180
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_tumour_15.e335639180
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_48
>> Job ID: 335639020
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_48.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_48.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_50
>> Job ID: 335639025
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_50.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_50.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_52
>> Job ID: 335639111
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_52.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_52.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_56
>> Job ID: 335639173
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_56.sh
>> Command exit code: 0
>> Contents Excerpt:
>> Command run:
>> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_34.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_34.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_38
>> Job ID: 335638783
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_38.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_38.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_42
>> Job ID: 335638805
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_42.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_42.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_46
>> Job ID: 335638826
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_46.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_46.stderr
>> -----------------------------------------------------------------------
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_unpackRef_NA_10.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_22
>> Job ID: 335638775
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_22.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_22.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_28
>> Job ID: 335638776
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_28.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_28.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_32
>> Job ID: 335638777
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_32.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_control_32.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_34
>> Job ID: 335638778
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-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/genera
>> ted-scripts/s58_unpackRef_NA_9.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_unpackRef_NA_9.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_verifyBamHomChk_control_6
>> Job ID: 331891143
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_verifyBamHomChk_control_6.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_verifyBamHomChk_control_6.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_basFileGenerate_control_11
>> Job ID: 332292910
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_basFileGenerate_control_11.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_basFileGenerate_control_11.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_unpackRef_NA_10
>> Job ID: 332292911
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_unpackRef_NA_10.sh
>> Command exit code: 0
>> Command run:
>> bash -lc /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_start_0.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_start_0.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_mark_start_1
>> Job ID: 331890603
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_mark_start_1.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_mark_start_1.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_prepBam_control_3
>> Job ID: 331890831
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_prepBam_control_3.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_prepBam_control_3.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_prepBam_tumour_2
>> Job ID: 331890832
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_prepBam_tumour_2.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_prepBam_tumour_2.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_ASCAT_allele_count_61.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_BRASS_input_99
>> Job ID: 379374477
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_BRASS_input_99.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_merge_59
>> Job ID: 379374478
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-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/genera
>> ted-scripts/s58_start_0.e331890362
>> Updated: Tue Sep 20 00:38:10 UTC 2016
>> Contents Excerpt:
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_renameSampleFile_208.o373317274
>> Updated: Tue Sep 20 12:08:37 UTC 2016
>> Contents Excerpt:
>> Modified command: cp /var/spool/cwl/b02b4bba-6e66-4
>> 4fb-a48f-38c309aaaac5.genotype.tar.gz /var/spool/cwl/b02b4bba-6e66-4
>> 4fb-a48f-38c309aaaac5.csc_0-0-0.20160920.somatic.genotype.tar.gz
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_renameSampleFile_208.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_57
>> Job ID: 373317275
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_57.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_ASCAT_allele_count_60
>> Job ID: 379374473
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-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/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_39.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_41
>> Job ID: 335639489
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_41.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_45
>> Job ID: 335639845
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_45.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_43
>> Job ID: 335639853
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-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/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_33.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_35
>> Job ID: 335639430
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_35.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_37
>> Job ID: 335639431
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_37.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_39
>> Job ID: 335639452
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_25.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_27
>> Job ID: 335639400
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_27.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_29
>> Job ID: 335639401
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_29.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_31
>> Job ID: 335639417
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_31.stdout
>> -----------------------------------------------------------------------
>> 23593416inputs+121608outputs (0major+421477minor)pagefaults 0swaps
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_tumour_17.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_15
>> Job ID: 335639180
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_15.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_19
>> Job ID: 335639200
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_19.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_23
>> Job ID: 335639375
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_tumour_23.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_25
>> Job ID: 335639387
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_bbAllele_tumour_25.o335639387
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_56
>> Job ID: 335639173
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_56.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_54
>> Job ID: 335639174
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_54.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_58
>> Job ID: 335639178
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_58.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_tumour_17
>> Job ID: 335639179
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_46.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_48
>> Job ID: 335639020
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_48.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_50
>> Job ID: 335639025
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_50.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_52
>> Job ID: 335639111
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_52.stdout
>> -----------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -6a3e-4a98-b41c-f8add599884c.11.tsv -b /var/spool/cwl/fdcb1bd7cffca69
>> d15383ca9566c58e0.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/genera
>> ted-scripts/s58_bbAllele_control_34.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_38
>> Job ID: 335638783
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_38.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_42
>> Job ID: 335638805
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_control_42.stdout
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_control_46
>> Job ID: 379374477
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_cgpPindel_input_70.sh
>>
>> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl
>> <http://UrlBlockedError.aspx> -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_mrg100
>> 0_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://UrlBlockedError.aspx> -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_mrg100
>> 0_no_exon_coreChrs.bed.gz
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_cgpPindel_input_70.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_merge_59
>> Job ID: 379374478
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_merge_59.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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_CgpS
>> omaticCore_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://UrlBlockedError.aspx>",
>> "class": "File"
>> },
>> "refFrom": {
>> "path": "https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/reference
>> /GRCh37d5_CGP_refBundle.tar.gz <http://UrlBlockedError.aspx>",
>> "class": "File"
>> },
>> "tumor": {
>> "path": "/home/ubuntu/DockerTest-Miguel/data/7875b5196f6b8b52847f99b
>> f370aada0.bam",
>> "class": "File"
>> },
>> "normal": {
>> "path": "/home/ubuntu/DockerTest-Miguel/data/fdcb1bd7cffca69d15383ca
>> 9566c58e0.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.verif
>> yBamId.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.imput
>> eCounts.tar.gz",
>> "class": "File"
>> },
>> "somatic_genotype_tar_gz": {
>> "path": "/home/ubuntu/DockerTest-Miguel/Sanger/results/somatic.genot
>> ype.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/genera
>> ted-scripts/s58_bbAllele_merge_59.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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_CgpS
>> omaticCore_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/genera
>> ted-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/genera
>> ted-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/genera
>> ted-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/genera
>> ted-scripts/s58_ASCAT_allele_count_61.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_cgpPindel_input_70
>> Job ID: 379374477
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_cgpPindel_input_70.sh
>>
>> Output from command: /usr/bin/perl /opt/wtsi-cgp/bin/pindel_input_gen.pl
>> <http://UrlBlockedError.aspx> -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_mrg100
>> 0_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://UrlBlockedError.aspx> -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_mrg100
>> 0_no_exon_coreChrs.bed.gz
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-scripts/s58_cgpPindel_input_70.stderr
>> -----------------------------------------------------------------------
>>
>> -----------------------------------------------------------------------
>> Job Name: s58_bbAllele_merge_59
>> Job ID: 379374478
>> File: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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/genera
>> ted-scripts/s58_bbAllele_merge_59.sh
>> Command exit code: 0
>>
>>
>> Full output: /datastore/oozie-729e0a3c-fd0e-46ee-8c3f-fde2322fe848/genera
>> ted-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_CgpS
>> omaticCore_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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