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).
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
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: |
|
||||||||||
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
}
|