Bug #13849
closed
[CWL] secondaryFiles checks failed in single container
0%
Description
single container
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-1vziek0s8udmajx
non-single container
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-g0u996tfq07d4mp
Note that the non-single container run failed, with the secondaryFiles checks prompted errors, as they should.
cwltool ERROR: Cannot make scatter job: Missing required secondary file 'chr1.1kg.phase3.v5a.vcf.gz.tbi' from file object: {
"basename": "chr1.1kg.phase3.v5a.vcf.gz",
"nameroot": "chr1.1kg.phase3.v5a.vcf",
"nameext": ".gz",
"location": "keep:ba7cd392bc4aa229c3c771b496e79628+9990/chr1.1kg.phase3.v5a.vcf.gz",
"secondaryFiles": [],
"class": "File"
}
This means the secondaryFiles checks failed in the single container version. See the attached tar ball for cwl. Run with
arvados-cwl-runner phasing-wf.cwl phasing-NA12878.yml
Files
Updated by Jiayong Li over 6 years ago
- File Phasing.tar.gz Phasing.tar.gz added
- Description updated (diff)
- Status changed from In Progress to New
Updated by Tom Morris over 6 years ago
- Assigned To set to Peter Amstutz
- Target version set to 2018-08-15 Sprint
Updated by Peter Amstutz over 6 years ago
The expectation is that it would fail when run with RunInSingleContainer, but it didn't fail.
The diagnosis is that RunInSingleContainer uses cwltool inside the container. If the version of cwltool is older, in isn't enforcing those checks.
The solution is to rebuild the container image with a newer arvados-cwl-runner / cwltool.