Hello,
I am new to WDL programming and running workflows on FireCloud.
I was trying to run a workflow using the BamToUnmappedRGBams method. However, I seem to be having a problem specifying the output directory (BamToUnmappedRGBamsWf.RevertBamToUnmappedRGBams.output_dir: (String)).
I've tried several different ways to specify the path to a directory I made in my Google bucket, but I keep getting the error:
message: Task BamToUnmappedRGBamsWf.RevertBamToUnmappedRGBams:NA:1 failed. JES error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/glob-3bcbe4e7489c90f75e0523ac6f3a9385/* -> gs://fc-03a666bd-8b66-48f0-9d3d-58c4ad173533/dfb35454-a867-4734-aeec-9411ac34780f/BamToUnmappedRGBamsWf/f577d5af-8dfe-43b5-95ce-77039a8902c2/call-RevertBamToUnmappedRGBams/glob-3bcbe4e7489c90f75e0523ac6f3a9385/ (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/glob-3bcbe4e7489c90f75e0523ac6f3a9385/* gs://fc-03a666bd-8b66-48f0-9d3d-58c4ad173533/dfb35454-a867-4734-aeec-9411ac34780f/BamToUnmappedRGBamsWf/f577d5af-8dfe-43b5-95ce-77039a8902c2/call-RevertBamToUnmappedRGBams/glob-3bcbe4e7489c90f75e0523ac6f3a9385/, command failed: CommandException: No URLs matched: /mnt/local-disk/glob-3bcbe4e7489c90f75e0523ac6f3a9385/*\nCommandException: 1 file/object could not be transferred.\n)"
Looking at the stderr.log output, I see:
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.Sy40DF
When OUTPUT_BY_READGROUP=true and OUTPUT is provided, it must be a directory: gs:/fc-03a666bd-8b66-48f0-9d3d-58c4ad173533/ubams
USAGE: RevertSam [options]
How can I specify the directory so that it is recognized? I've looked at a number of public workspaces, but can't seem to find an example.
Thank you for your help!
All the best,
Kate