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?

Thanks.

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
(gs://fc-f7b0068e-1a0b-4af5-b85f-d4855360f18c/99c3ce18-bc08-4528-abe9-40f01d78f4ba/TumorNormalBloodBiopsyPipeline/49b2c644-b416-4d4d-bd6d-0d0e45b030d0/call-Mutect2Gatk4/shard-46/Mutect2Gatk4-46-stderr.log)
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 ->
gs://fc-f7b0068e-1a0b-4af5-b85f-d4855360f18c/99c3ce18-bc08-4528-abe9-40f01d78f4ba/TumorNormalBloodBiopsyPipeline/49b2c644-b416-4d4d-bd6d-0d0e45b030d0/call-Mutect2Gatk4/shard-46/HapMap_1__spike_2.vcf
(cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log
/mnt/local-disk/HapMap_1__spike_2.vcf
gs://fc-f7b0068e-1a0b-4af5-b85f-d4855360f18c/99c3ce18-bc08-4528-abe9-40f01d78f4ba/TumorNormalBloodBiopsyPipeline/49b2c644-b416-4d4d-bd6d-0d0e45b030d0/call-Mutect2Gatk4/shard-46/HapMap_1__spike_2.vcf,
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

Answers

  • 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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