The flow with example files fails

[mgcam]

verifyBamID used in the docker container seems to be verifyBamID2, which is known to be much less tolerant to low depth. The workflow with default sample files fails at the contamination detection stage.

[moschetti]

Also seeing the workflow failing on CheckContamination.

Get warnings for insufficient markings and then errors during delocalization, although not sure if those are related. The following is from the end of CheckContamination.log:

[...]
NOTICE - Process chr22:50745507-50745507...
NOTICE - Process chr22:50774185-50774185...
NOTICE - Number of marker in Reference Matrix:99976
NOTICE - Number of marker shared with input file:331
NOTICE - Mean Depth:1.003021
NOTICE - SD Depth:0.054882
NOTICE - 330 SNP markers remained after sanity check.

�WARNING -
Insufficient Available markers, check input bam depth distribution in output pileup file after specifying --OutputPileup
2019/08/21 22:33:10 Starting delocalization.
2019/08/21 22:33:11 Delocalizing output /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM -> gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/NA12878_PLUMBING.preBqsr.selfSM
2019/08/21 22:33:14 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/ failed
CommandException: No URLs matched: /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM
2019/08/21 22:33:14 Waiting 5 seconds and retrying
2019/08/21 22:33:20 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/ failed
CommandException: No URLs matched: /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM
2019/08/21 22:33:20 Waiting 5 seconds and retrying
2019/08/21 22:33:26 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/ failed
CommandException: No URLs matched: /cromwell_root/NA12878_PLUMBING.preBqsr.selfSM
2019/08/21 22:33:28 Delocalizing output /cromwell_root/stdout -> gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/stdout
2019/08/21 22:33:32 Delocalizing output /cromwell_root/stderr -> gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/stderr
2019/08/21 22:33:37 Delocalizing output /cromwell_root/rc -> gs:////work/WholeGenomeGermlineSingleSample/795f578d-3944-406f-b15e-933c4043f65e/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/7197d913-456d-411d-bf05-1164c1549aeb/call-CheckContamination/rc

[mgcam]

Yes this is exactly the error I had. Most likely, veryfyBamID exist abnormally without creating the expected output - *.selfSM file. What you see is an error to copy the file back to the bucket.

[ghost]

Any updates on this? I get the same error.