Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Latest Release: 05/01/19
Release Notes can be found here.

Error Firecloud joint-discovery-gatk4

Hi,

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!

Best Answer

Answers

Sign In or Register to comment.