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Error Firecloud joint-discovery-gatk4


I am running joint-discovery-gatk4 (snapshot 11) on firecloud for 900 TCGA WES samples, and keep on getting the following errors:

message: Task JointGenotyping.ImportGVCFs:412:1 failed. Job exit code 1. Check gs://fc-3ce59332-1fac-47da-92a3-c1bbf98aedc7/873e3124-95be-4023-914b-426fb65e0269/JointGenotyping/22070ee3-719d-440d-888e-bfec49bdb5f6/call-ImportGVCFs/shard-412/stderr for more information. PAPI error code 5. 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/genomicsdb.tar -> gs://fc-3ce59332-1fac-47da-92a3-c1bbf98aedc7/873e3124-95be-4023-914b-426fb65e0269/JointGenotyping/22070ee3-719d-440d-888e-bfec49bdb5f6/call-ImportGVCFs/shard-412/genomicsdb.tar (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/genomicsdb.tar gs://fc-3ce59332-1fac-47da-92a3-c1bbf98aedc7/873e3124-95be-4023-914b-426fb65e0269/JointGenotyping/22070ee3-719d-440d-888e-bfec49bdb5f6/call-ImportGVCFs/shard-412/genomicsdb.tar, command failed: CommandException: No URLs matched: /mnt/local-disk/genomicsdb.tar\nCommandException: 1 file/object could not be transferred.\n)"

I run the haplotypecaller-gvcf-gatk4 (snapshot 13) first, and it run successfully. But for "joint-discovery-gatk4" it always get the error and the log file is empty. I select 20 sample (out of the 900) and run the pipeline, and it works well.

I shared the workspace with [email protected] Submission id 873e3124-95be-4023-914b-426fb65e0269 is the failed one (for the 900 samples), and submission id 40880417-f5fe-4cde-a6e9-5be0d70356fc is the succeeded one for the 20 test samples (but it also failed for several times and I have to resubmit, and in the end succeeded).

Would you please help to check or give suggestions? Thank you a lot!

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