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Failure to delocalize file - how to specify a directory in FireCloud method config?

kmegqkmegq BroadMember, Broadie

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

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Best Answers

  • kmegqkmegq BroadMember, Broadie
    Accepted Answer

    Hi Tiffany,

    Aha, I think I've figured it out. I was trying to pass in a Google bucket location, when I needed to specify a local disk location. After searching again, I found an example configuration, which simply passes in "." as the directory path, and that seems to work!

    Thank you!
    Kate

  • kmegqkmegq BroadMember, Broadie
    Accepted Answer

    The method configuration was here:
    https://portal.firecloud.org/#methods/c/vdauwera/BamToUnmappedRGBams_MC/1

    And the relevant line is:

    RevertBamToUnmappedRGBams    output_dir    String  "."
    

    Best,
    Kate

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Broadie, Moderator

    Hi @kmegq
    Can you attach a screenshot of your outputs specified in the method config? To confirm, you want the output files to be placed into a Google bucket that is not the Google bucket of the workspace you are running the method in?

    Thanks,
    Tiffany

  • kmegqkmegq BroadMember, Broadie
    Accepted Answer

    Hi Tiffany,

    Aha, I think I've figured it out. I was trying to pass in a Google bucket location, when I needed to specify a local disk location. After searching again, I found an example configuration, which simply passes in "." as the directory path, and that seems to work!

    Thank you!
    Kate

  • kmegqkmegq BroadMember, Broadie
    Accepted Answer

    The method configuration was here:
    https://portal.firecloud.org/#methods/c/vdauwera/BamToUnmappedRGBams_MC/1

    And the relevant line is:

    RevertBamToUnmappedRGBams    output_dir    String  "."
    

    Best,
    Kate

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