Bug #9755

[CWL] Creating intermediate folders in working directory (fails in cwl-runner)

Added by Bharath Manicka Vasagam about 4 years ago. Updated almost 4 years ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
Crunch
Target version:
Start date:
08/08/2016
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

I am working on a cwltool wrapper for a tool that is based on java.

Running cwltool locally creates a following gist

[ALEA] [createGenome] Started at [Mon Aug 8 13:46:32 UTC 2016]
INFO [2016-08-08 13:46:33,073]  [TrackLoader.java:118] [main]  Loading resource, path /var/lib/cwl/stg881559db-db95-446d-a2b9-423950f78e05/mgp.v2.snps.chrname.vcf.gz
Aug 08, 2016 1:46:33 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
INFO [2016-08-08 13:46:33,402]  [DirectoryManager.java:163] [main]  IGV Directory: /var/spool/cwl/?/igv

[FastaWriter] Creating output/CASTEiJ.snps.fasta

But running the same with arvados cwl-runner gives the following gist

2016-08-08_14:16:09 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr [ALEA] [createGenome] Started at [Mon Aug 8 14:16:09 UTC 2016]
2016-08-08_14:16:10 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr INFO [2016-08-08 14:16:10,289]  [TrackLoader.java:118] [main]  Loading resource, path /keep/a72ef131bfd2b55f6172551e3a6e58be+3627/mgp.v2.snps.chrname.vcf.gz
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr Aug 08, 2016 2:16:12 PM java.util.prefs.FileSystemPreferences$1 run
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr WARNING: Couldn't create user preferences directory. User preferences are unusable.
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr Aug 08, 2016 2:16:12 PM java.util.prefs.FileSystemPreferences$1 run
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr WARNING: java.io.IOException: No such file or directory
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr ERROR [2016-08-08 14:16:12,196]  [DirectoryManager.java:121] [main]  Failed to create user directory!
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr ERROR [2016-08-08 14:16:12,397]  [TrackLoader.java:256] [main]  
2016-08-08_14:16:12 29rky-8i9sb-w48pvug1dmlo4cd 11053 0 stderr No X11 DISPLAY variable was set, but this program performed an operation which requires it.

History

#1 Updated by Tom Morris almost 4 years ago

  • Subject changed from Creating intermediate folders in working directory (fails in cwl-runner) to [CWL] Creating intermediate folders in working directory (fails in cwl-runner)
  • Target version set to Arvados Future Sprints

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