Can't Localize File in Google Storage Bucket (No URL)

amr@broadinstitute.orgeamr@broadinstitute.orge Member, Broadie
edited May 1 in Ask the WDL team

I have a task in a WDL that takes as input a GVCF file located in a bucket. The task fails to start with this error:

Failures: [{"message": "Workflow failed"
"causedBy": [{"message": "Task gatk_process_cohort.gatk_joint_genotype_task:NA:1 failed. The job was stopped before the command finished. PAPI error code 5. Message: 9: Failed to localize files: failed to copy the following files: \"gs://broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf\\t\\r -> /mnt/local-disk/broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf\\t\\r (cp failed: gsutil -q -m cp gs://broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf\\t\\r /mnt/local-disk/broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf\\t\\r
command failed: CommandException: No URLs matched: gs://broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf\\t\\r\\nCommandException: 1 file/object could not be trans ferred.\\n)\""

The file in question, 'gs://broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf' does exist in this location as seen by a gsutil ls command:

12:28pm amr@stout ~ $ gsutil ls gs://broad-cil-devel-bucket/broad-file-inputs/G:/Candida_Auris.gvcf
9.125u 1.536s 0:12.65 84.1%     0+0k 16+40io 2pf+0w
12:28pm amr@stout ~ $ 

So I'm at a loss as to why this error is occurring. Any help appreciated!


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