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Bug #9659

closed

[CWL] Jobs crash when arvados/jobs:latest is not suitable to run CWL jobs

Added by Radhika Chippada over 8 years ago. Updated 4 months ago.

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.


Related issues 1 (0 open1 closed)

Related to Arvados - Idea #9677: [Docs] Install guide needs to create arvados/jobs:latest Docker image as a standard objectResolvedWard Vandewege07/29/2016Actions
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