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Bug #9659
closed[CWL] Jobs crash when arvados/jobs:latest is not suitable to run CWL jobs
Status:
Resolved
Priority:
Normal
Assigned To:
-
Category:
SDKs
Target version:
-
Story points:
-
Description
It appears that the cwl documentation may be out of sync with latest arvados-cwl-runner code updates.
$ arvados-cwl-runner --debug bwa-mem.cwl bwa-mem-input.yml /data/scratch/brett/cwl/bin/arvados-cwl-runner 1.0.20160717133709, arvados-python-client 0.1.20160721023501, cwltool 1.0.20160714182449 2016-07-26 19:02:49 arvados.arv-run[43558] INFO: Upload local files: "bwa-mem.cwl" 2016-07-26 19:02:50 arvados.arv-run[43558] INFO: Uploaded to qr1hi-4zz18-yyrz0vbtn8iuuif 2016-07-26 19:02:59 arvados.cwl-runner[43558] INFO: Submitted job qr1hi-8i9sb-vvdfe70pw0oucch 2016-07-26 19:03:06 arvados.cwl-runner[43558] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-vvdfe70pw0oucch) is Running 2016-07-26 19:03:21 arvados.cwl-runner[43558] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-vvdfe70pw0oucch) is Failed 2016-07-26 19:03:21 arvados.cwl-runner[43558] ERROR: While getting final output object: [Errno 2] File not found 2016-07-26 19:03:21 arvados.cwl-runner[43558] WARNING: Overall process status is permanentFail Workflow error, try again with --debug for more information: Workflow failed. Traceback (most recent call last): File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/cwltool/main.py", line 707, in main **vars(args)) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/__init__.py", line 222, in arvExecutor raise WorkflowException("Workflow failed.") WorkflowException: Workflow failed.
This error occurs consistently whether or not I use --debug
.
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