{"action":"created","issue":{"url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5","repository_url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker","labels_url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5/comments","events_url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5/events","html_url":"https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5","id":174797262,"number":5,"title":"test data - 2","user":{"login":"denis-yuen","id":1730679,"avatar_url":"https://avatars.githubusercontent.com/u/1730679?v=3","gravatar_id":"","url":"https://api.github.com/users/denis-yuen","html_url":"https://github.com/denis-yuen","followers_url":"https://api.github.com/users/denis-yuen/followers","following_url":"https://api.github.com/users/denis-yuen/following{/other_user}","gists_url":"https://api.github.com/users/denis-yuen/gists{/gist_id}","starred_url":"https://api.github.com/users/denis-yuen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/denis-yuen/subscriptions","organizations_url":"https://api.github.com/users/denis-yuen/orgs","repos_url":"https://api.github.com/users/denis-yuen/repos","events_url":"https://api.github.com/users/denis-yuen/events{/privacy}","received_events_url":"https://api.github.com/users/denis-yuen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"briandoconnor","id":1730584,"avatar_url":"https://avatars.githubusercontent.com/u/1730584?v=3","gravatar_id":"","url":"https://api.github.com/users/briandoconnor","html_url":"https://github.com/briandoconnor","followers_url":"https://api.github.com/users/briandoconnor/followers","following_url":"https://api.github.com/users/briandoconnor/following{/other_user}","gists_url":"https://api.github.com/users/briandoconnor/gists{/gist_id}","starred_url":"https://api.github.com/users/briandoconnor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/briandoconnor/subscriptions","organizations_url":"https://api.github.com/users/briandoconnor/orgs","repos_url":"https://api.github.com/users/briandoconnor/repos","events_url":"https://api.github.com/users/briandoconnor/events{/privacy}","received_events_url":"https://api.github.com/users/briandoconnor/received_events","type":"User","site_admin":false},"assignees":[{"login":"briandoconnor","id":1730584,"avatar_url":"https://avatars.githubusercontent.com/u/1730584?v=3","gravatar_id":"","url":"https://api.github.com/users/briandoconnor","html_url":"https://github.com/briandoconnor","followers_url":"https://api.github.com/users/briandoconnor/followers","following_url":"https://api.github.com/users/briandoconnor/following{/other_user}","gists_url":"https://api.github.com/users/briandoconnor/gists{/gist_id}","starred_url":"https://api.github.com/users/briandoconnor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/briandoconnor/subscriptions","organizations_url":"https://api.github.com/users/briandoconnor/orgs","repos_url":"https://api.github.com/users/briandoconnor/repos","events_url":"https://api.github.com/users/briandoconnor/events{/privacy}","received_events_url":"https://api.github.com/users/briandoconnor/received_events","type":"User","site_admin":false}],"milestone":null,"comments":2,"created_at":"2016-09-02T16:20:20Z","updated_at":"2016-09-02T17:30:02Z","closed_at":null,"body":"Currently attempting to execute the workflow with the test data on the branch https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/tree/feature/cwl1\r\n\r\nCommand is \r\n```\r\ndockstore tool launch --entry Dockstore.cwl --local-entry --json test2.json\r\n```\r\nwhich becomes \r\n```\r\n[job Dockstore.cwl] /tmp/tmp510v1N$ docker \\                                                                                                                                                             [1536/1663]\r\n    run \\\r\n    -i \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/ef2387e1-00c2-497e-9bae-19d833273d70/9f8f6f03df6d100c90a761164800a42c.bam:/var/lib/cwl/stg86779b72-335\r\n2-4adf-8478-98e3853b440f/9f8f6f03df6d100c90a761164800a42c.bam:ro \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/196da89e-6d8a-49af-9ab2-70d302816e29/GRCh37d5_battenberg.tar.gz:/var/lib/cwl/stg6f32c8f1-139e-43cd-b94\r\n7-427fdd812590/GRCh37d5_battenberg.tar.gz:ro \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/ef2387e1-00c2-497e-9bae-19d833273d70/9f8f6f03df6d100c90a761164800a42c.bam.bai:/var/lib/cwl/stg86779b72\r\n-3352-4adf-8478-98e3853b440f/9f8f6f03df6d100c90a761164800a42c.bam.bai:ro \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/ca7276bf-10fa-45b8-9634-1b6d04270b99/ad4aeedc224c6be5e21e26c038a43df4.bam.bai:/var/lib/cwl/stg78f59412\r\n-5cf5-4473-b80e-1720be3192c4/ad4aeedc224c6be5e21e26c038a43df4.bam.bai:ro \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/ca7276bf-10fa-45b8-9634-1b6d04270b99/ad4aeedc224c6be5e21e26c038a43df4.bam:/var/lib/cwl/stg78f59412-5cf\r\n5-4473-b80e-1720be3192c4/ad4aeedc224c6be5e21e26c038a43df4.bam:ro \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/./datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/inputs/e1b2a106-3fe8-4e2b-9159-33c5ce9c95d6/GRCh37d5_CGP_refBundle.tar.gz:/var/lib/cwl/stg4d74f530-1cd7-4de3-\r\n835f-7de7820a2dab/GRCh37d5_CGP_refBundle.tar.gz:ro \\\r\n    --volume=/tmp/tmp510v1N:/var/spool/cwl:rw \\\r\n    --volume=/home/ubuntu/CGP-Somatic-Docker/datastore/launcher-86c12006-c63e-4ebe-880f-f248b0e76b97/workinguyrgqy:/tmp:rw \\\r\n    --workdir=/var/spool/cwl \\\r\n    --read-only=true \\\r\n    --user=1000 \\\r\n    --rm \\\r\n    --env=TMPDIR=/tmp \\\r\n    --env=HOME=/var/spool/cwl \\\r\n    quay.io/pancancer/pcawg-sanger-cgp-workflow:feature_cwl1 \\\r\n    python \\\r\n    /home/seqware/CGP-Somatic-Docker/scripts/run_seqware_workflow.py \\\r\n    --tumor \\\r\n    /var/lib/cwl/stg78f59412-5cf5-4473-b80e-1720be3192c4/ad4aeedc224c6be5e21e26c038a43df4.bam \\\r\n    --normal \\\r\n    /var/lib/cwl/stg86779b72-3352-4adf-8478-98e3853b440f/9f8f6f03df6d100c90a761164800a42c.bam \\\r\n    --refFrom \\\r\n    /var/lib/cwl/stg4d74f530-1cd7-4de3-835f-7de7820a2dab/GRCh37d5_CGP_refBundle.tar.gz \\\r\n    --bbFrom \\\r\n    /var/lib/cwl/stg6f32c8f1-139e-43cd-b947-427fdd812590/GRCh37d5_battenberg.tar.gz\r\n```\r\n\r\nLooking at \r\nhttps://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/Dockstore_cwl.json\r\n\r\ncorresponds to \r\n\r\nhttps://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/feature/cwl1/test2.json\r\n\r\nCurrently fails with the following messages\r\n```\r\n[2016/09/02 11:59:54] | Row #7 , Attempt #1 out of 1 : s58_ASCAT_ascat_62,s58_BRASS_cover_101,s58_cgpPindel_pindel_71,s58_renameSampleFile_213,s58_renameSampleFile_214\r\n[2016/09/02 11:59:54] |         Submitting 26480M batch with: s58_ASCAT_ascat_62,s58_BRASS_cover_101,s58_cgpPindel_pindel_71,s58_renameSampleFile_213,s58_renameSampleFile_214\r\n[2016/09/02 11:59:54] |         Running command: bash /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_renameSampleFile_213-runner.sh\r\n[2016/09/02 11:59:54] |         Running command: bash /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_BRASS_cover_101-runner.sh\r\n[2016/09/02 11:59:54] |         Running command: bash /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_renameSampleFile_214-runner.sh\r\n[2016/09/02 11:59:54] |         Running command: bash /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_ASCAT_ascat_62-runner.sh\r\n[2016/09/02 11:59:54] |         Running command: bash /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_cgpPindel_pindel_71-runner.sh\r\n[2016/09/02 11:59:59] |         Workflow step succeeded: s58_renameSampleFile_214\r\n[2016/09/02 12:00:15] |         Workflow step succeeded: s58_renameSampleFile_213\r\n[2016/09/02 12:38:13] |         Workflow step failed: s58_ASCAT_ascat_62\r\n[2016/09/02 13:37:31] |         Workflow step succeeded: s58_BRASS_cover_101\r\n[2016/09/02 15:22:18] |         Workflow step succeeded: s58_cgpPindel_pindel_71\r\n[2016/09/02 15:22:18] | Setting workflow-run status to failed for: 58\r\n[--plugin, io.seqware.pipeline.plugins.WorkflowWatcher, --, --workflow-run-accession, 58]\r\nFound local reference archive: /var/lib/cwl/stg4d74f530-1cd7-4de3-835f-7de7820a2dab/GRCh37d5_CGP_refBundle.tar.gz\r\nFound local reference archive: /var/lib/cwl/stg6f32c8f1-139e-43cd-b947-427fdd812590/GRCh37d5_battenberg.tar.gz\r\nWorkflow run 58 is currently failed\r\n\r\n```\r\n\r\n```\r\nJob Name: s58_ASCAT_ascat_62\r\nJob ID:   817594229\r\nFile:     /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_ASCAT_ascat_62.o817594229\r\nUpdated:  Fri Sep 02 12:38:13 UTC 2016\r\nContents Excerpt:\r\nCalls: ascat.plotRawData -> png\r\nIn addition: Warning message:\r\nIn png(filename = paste(ASCATobj$samples[i], \".tumour.png\", sep = \"\"),  :\r\n  unable to open connection to X11 display ''\r\nExecution halted\r\n\"cd /var/spool/cwl/0/ascat/tmpAscat/ascat; /opt/wtsi-cgp/bin/Rscript /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Asca\r\nt-Implement/ascat /var/spool/cwl/reference_files/ascat/SnpPositions.tsv /var/spool/cwl/reference_files/ascat/SnpGcCorrections.tsv fc969f27-bdc3-cd03-e040-11ac0c48577e fc969f27-bdc3-cd03-e040-11ac0c48577e.count fc\r\n969f27-bdc6-cd03-e040-11ac0c48577e fc969f27-bdc6-cd03-e040-11ac0c48577e.count XX /var/spool/cwl/0/ascat/tmpAscat/ascat/fc969f27-bdc3-cd03-e040-11ac0c48577e.Rdata\" unexpectedly returned exit value 1 at (eval 294) \r\nline 13.\r\n at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 190\r\nCommand exited with non-zero status 2\r\n597.47user 7.46system 38:15.68elapsed 26%CPU (0avgtext+0avgdata 6048784maxresident)k\r\n662816inputs+209168outputs (130major+435707minor)pagefaults 0swaps\r\nCalls: ascat.plotRawData -> png\r\nIn addition: Warning message:\r\nIn png(filename = paste(ASCATobj$samples[i], \".tumour.png\", sep = \"\"),  :\r\n  unable to open connection to X11 display ''\r\nExecution halted\r\n\"cd /var/spool/cwl/0/ascat/tmpAscat/ascat; /opt/wtsi-cgp/bin/Rscript /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Asca\r\nt-Implement/ascat /var/spool/cwl/reference_files/ascat/SnpPositions.tsv /var/spool/cwl/reference_files/ascat/SnpGcCorrections.tsv fc969f27-bdc3-cd03-e040-11ac0c48577e fc969f27-bdc3-cd03-e040-11ac0c48577e.count fc\r\n969f27-bdc6-cd03-e040-11ac0c48577e fc969f27-bdc6-cd03-e040-11ac0c48577e.count XX /var/spool/cwl/0/ascat/tmpAscat/ascat/fc969f27-bdc3-cd03-e040-11ac0c48577e.Rdata\" unexpectedly returned exit value 1 at (eval 294) \r\nline 13.\r\n at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 190\r\nCommand exited with non-zero status 2\r\n597.47user 7.46system 38:15.68elapsed 26%CPU (0avgtext+0avgdata 6048784maxresident)k\r\n662816inputs+209168outputs (130major+435707minor)pagefaults 0swaps\r\nThe method 'do_run' exited abnormally so the Runner will terminate here!\r\nReturn value was: 1\r\n\r\nFull output: /datastore/oozie-6ddf193c-472f-42ee-a74a-6cc6ce66e7f2/generated-scripts/s58_ASCAT_ascat_62.stdout\r\n```\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/comments/244438336","html_url":"https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5#issuecomment-244438336","issue_url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/issues/5","id":244438336,"user":{"login":"adamstruck","id":5560701,"avatar_url":"https://avatars.githubusercontent.com/u/5560701?v=3","gravatar_id":"","url":"https://api.github.com/users/adamstruck","html_url":"https://github.com/adamstruck","followers_url":"https://api.github.com/users/adamstruck/followers","following_url":"https://api.github.com/users/adamstruck/following{/other_user}","gists_url":"https://api.github.com/users/adamstruck/gists{/gist_id}","starred_url":"https://api.github.com/users/adamstruck/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamstruck/subscriptions","organizations_url":"https://api.github.com/users/adamstruck/orgs","repos_url":"https://api.github.com/users/adamstruck/repos","events_url":"https://api.github.com/users/adamstruck/events{/privacy}","received_events_url":"https://api.github.com/users/adamstruck/received_events","type":"User","site_admin":false},"created_at":"2016-09-02T17:30:02Z","updated_at":"2016-09-02T17:30:02Z","body":"I think I have encountered this error before when I was developing the WDL version... It occurred when the .Rprofile file wasn't being loaded by R because I had changed the home directory. "}}
{"actor":{"display_login":"adamstruck"}}