This container started at 2021-06-16 19:47:17 UTC. It failed after 1m at 2021-06-16 19:48:46 UTC. Check the error information below.

It has runtime of 0m20s(1mqueued) and used 0m20s of node allocation time (1.0⨯ scaling).

Failed

Error: arvados.cwl-runner: [container workflow.json#main] (pirca-xvhdp-s52rth4npffa5zp) error log: (and 1 more) 

  2021-06-16T19:48:15.102948472Z crunch-run crunch-run 2.2.0 (go1.16.3) started
  2021-06-16T19:48:15.102999410Z crunch-run Executing container 'pirca-dz642-7hc4igolissn5oh'
  2021-06-16T19:48:15.103010058Z crunch-run Executing on host 'ip-10-254-254-84'
  2021-06-16T19:48:15.188750604Z crunch-run Fetching Docker image from collection '2975e1250c18c7a8becb73ddce572480+134'
  2021-06-16T19:48:15.206050230Z crunch-run Using Docker image id 'sha256:8993688148d9178dd5b0076e8924f604074bb4b73b6dab0b163e19db0ada4607'
  2021-06-16T19:48:15.206851288Z crunch-run Loading Docker image from keep
  2021-06-16T19:48:16.879249955Z crunch-run Docker response: {"stream":"Loaded image ID: sha256:8993688148d9178dd5b0076e8924f604074bb4b73b6dab0b163e19db0ada4607\n"}
  2021-06-16T19:48:16.879459532Z crunch-run Running [arv-mount --foreground --allow-other --read-write --crunchstat-interval=10 --file-cache 268435456 --mount-by-pdh by_id /tmp/crunch-run.pirca-dz642-7hc4igolissn5oh.602395099/keep946110334]
  2021-06-16T19:48:17.219802403Z crunch-run Creating Docker container
  2021-06-16T19:48:17.324166684Z crunch-run Attaching container streams
  2021-06-16T19:48:17.431854735Z crunch-run Starting Docker container id 'c33799de8f8333d3387bdbbf317f1be2bfd6afba6d4fd342e11a82ba06a8b62d'
  2021-06-16T19:48:17.966365541Z stdout Jun 16 19:48:17 ..... started STAR run
  2021-06-16T19:48:17.966365541Z stdout Jun 16 19:48:17 ... starting to generate Genome files
  2021-06-16T19:48:17.999107080Z crunch-run Waiting for container to finish
  2021-06-16T19:48:26.183719592Z stdout Jun 16 19:48:26 ..... processing annotations GTF
  2021-06-16T19:48:26.772909733Z stderr !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=249250621, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 12
  2021-06-16T19:48:28.051244250Z stdout Jun 16 19:48:28 ... starting to sort Suffix Array. This may take a long time...
  2021-06-16T19:48:29.373901774Z stdout Jun 16 19:48:29 ... sorting Suffix Array chunks and saving them to disk...
  2021-06-16T19:48:29.376258632Z stderr terminate called after throwing an instance of 'std::bad_alloc'
  2021-06-16T19:48:29.376258632Z stderr   what():  std::bad_alloc
  2021-06-16T19:48:32.260611006Z crunch-run Container exited with code: 139
  2021-06-16T19:48:32.277278946Z crunch-run copying "/_STARtmp/.keep" (0 bytes)
  2021-06-16T19:48:32.277359840Z crunch-run copying "/core" (510050304 bytes)
  2021-06-16T19:48:35.638936137Z crunch-run copying "/hg19-STAR-index/Log.out" (2993 bytes)
  2021-06-16T19:48:35.640508974Z crunch-run copying "/hg19-STAR-index/chrLength.txt" (10 bytes)
  2021-06-16T19:48:35.641215862Z crunch-run copying "/hg19-STAR-index/chrName.txt" (5 bytes)
  2021-06-16T19:48:35.641876382Z crunch-run copying "/hg19-STAR-index/chrNameLength.txt" (15 bytes)
  2021-06-16T19:48:35.642580535Z crunch-run copying "/hg19-STAR-index/chrStart.txt" (12 bytes)
  2021-06-16T19:48:35.643158351Z crunch-run copying "/hg19-STAR-index/exonGeTrInfo.tab" (1123248 bytes)
  2021-06-16T19:48:35.653183835Z crunch-run copying "/hg19-STAR-index/exonInfo.tab" (573122 bytes)
  2021-06-16T19:48:35.657092960Z crunch-run copying "/hg19-STAR-index/geneInfo.tab" (69585 bytes)
  2021-06-16T19:48:35.658543819Z crunch-run copying "/hg19-STAR-index/sjdbList.fromGTF.out.tab" (632839 bytes)
  2021-06-16T19:48:35.663954297Z crunch-run copying "/hg19-STAR-index/transcriptInfo.tab" (208431 bytes)
  2021-06-16T19:48:37.572832098Z crunch-run Complete

Warning: cwltool: Final process status is permanentFail

No detailed information available.

uuid: pirca-dz642-vhga0uohe8r1aw1
modified_by_user_uuid: pirca-tpzed-000000000000000
created_at: 2021-06-16 19:47:05 UTC
started_at: 2021-06-16 19:47:17 UTC
finished_at: 2021-06-16 19:48:46 UTC
outputs: db242187177e01ea447c3c0b69a1b652+382
priority: 562948329548486521
runtime_constraints:
API true
cuda {:device_count=>0, :driver_version=>"", :hardware_capability=>""}
keep_cache_ram 268435456
ram 1342177280
vcpus 1
docker_image_locator: af41a455939e61edb3a11aafce28be9a+261
command:
[ "arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps", "--disable-validate", "--disable-color", "--eval-timeout=20", "--thread-count=1", "--disable-reuse", "--collection-cache-size=256", "--on-error=continue", "--project-uuid=pirca-j7d0g-esxj0i6rwqci132", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" ]
cwl.input.json:
{ "Gtf": { "basename": "chr1-hg19_genes.gtf", "class": "File", "location": "keep:bcca5ee5b64d1f30296f204be49fc050+270/chr1-hg19_genes.gtf", "size": 10808303 }, "IndexName": "hg19-STAR-index", "InputFiles": [ { "basename": "chr1.fa", "class": "File", "format": "http://edamontology.org/format_1930", "location": "keep:bcca5ee5b64d1f30296f204be49fc050+270/chr1.fa", "size": 254235640 } ], "Overhang": 99 }

workflow.json#main

Failed
0m20s / 0m20s (1.0⨯)
Container requests
STAR-index-broken.cwl created at 2021-06-16 19:47:05 UTC.