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Failure to delocalize file, and failures due to invalid google credentials

flehartyfleharty Member, Broadie, Dev ✭✭
edited May 2017 in Ask the FireCloud Team

In my recent firecloud runs I've had a few jobs fail. The following two errors have happened multiple times, but I give just one example of each. Are there any suggestions for dealing with each of these errors?


Failed to delocalize file.

Submission ID: 99c3ce18-bc08-4528-abe9-40f01d78f4ba
Workflow ID: 49b2c644-b416-4d4d-bd6d-0d0e45b030d0

"message": "It appears that some of the expected output files for task
TumorNormalBloodBiopsyPipeline.Mutect2Gatk4:46:1 did not exist when
the command exited.\nA few things to try\n1) Check that the output
section in your WDL is correct. Remember that all output files
declared in a task must exist when the command exits.\n2) Check that
the return code is available and is valid with respect to your command
expected exit code\n3) Look into the stderr
file for evidence that some of the output files the command is
expected to create were not created.\n Failed to delocalize files:
failed to copy the following files:
\"/mnt/local-disk/HapMap_1__spike_2.vcf ->
(cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log
command failed: CommandException: No URLs matched:
/mnt/local-disk/HapMap_1__spike_2.vcf\nCommandException: 1
file/object could not be transferred.\n)"

Google Credentials are Invalid

Submission ID: cea28c0f-ee5d-4e8b-b693-c6da5ee01859
Workflow ID: 212dee26-d577-45c7-8bfe-3d8ad0386a4a
"message": "Google credentials are invalid: Read timed out"

Best Answer


  • flehartyfleharty Member, Broadie, Dev ✭✭

    The issues I was having with Google Credentials being Invalid were on my own files, but it is not something I've seen in the past week, so I suspect whatever the issue was, it has been resolved.

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