"Could not capture docker logs" error
I'm encountering an error I can't explain while testing a new method (MELT; see http://melt.igs.umaryland.edu/) on a single ~30X human whole-genome sample in FireCloud.
The error message returned in the Monitor tab is:
"message: Task MELTWorkflow.MELT:NA:1 failed. JES error code 10. Message: 15: Gsutil failed: Could not capture docker logs: failed to acquire logs: exit status 1"
The stdout and stderr logs for this job look completely normal, except the execution of the job appears to have suddenly stopped midway after running for >1 hour and exited without any obvious errors.
I wasn't able to find any leads for this error on Google or by searching here in the FireCloud forum.
The error message mentions Docker logs, but I've confirmed that the Docker image I deploy in the WDL runs successfully on my local machine, so I can't spot anything obviously wrong there either.
I've run this script on both the Broad and Partners Healthcare clusters on thousands of human WGS libraries previously without problems.
For reference, the Docker is on Dockerhub here:
I've also attached both the WDL and a script called from within the WDL. (Note: I had to upload both with a .txt extension as the forum kicked back errors when trying to upload files with .sh or .wdl extensions)
Please let me know if there's a clear solution to this error, or if there's any further information I can provide to help troubleshoot this bug. I'd appreciate any pointers or tips you can provide!
PhD Candidate, Talkowski Lab
MGH / Broad / HMS