Hello,
I was running haplotypecaller_gvcf_gatk4 for four samples in the same workspace. All but one finished the analysis. Message for the failed sample (all 50 shards) is as the following,
Task HaplotypeCallerGvcf_GATK4.HaplotypeCaller:5:1 failed. Job exit code 1. Check gs://fc-8da20bb3-0689-423f-b94b-8c196afd7a82/17ad2991-dab2-45c7-a68f-d5a31995f9c4/HaplotypeCallerGvcf_GATK4/5c9a1b93-7f39-424f-950e-70542e19e0b1/call-HaplotypeCaller/shard-5/HaplotypeCaller-5-stderr.log for more information. PAPI error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/HB3hg382.g.vcf.gz -> gs://fc-8da20bb3-0689-423f-b94b-8c196afd7a82/17ad2991-dab2-45c7-a68f-d5a31995f9c4/HaplotypeCallerGvcf_GATK4/5c9a1b93-7f39-424f-950e-70542e19e0b1/call-HaplotypeCaller/shard-5/HB3hg382.g.vcf.gz (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/HB3hg382.g.vcf.gz gs://fc-8da20bb3-0689-423f-b94b-8c196afd7a82/17ad2991-dab2-45c7-a68f-d5a31995f9c4/HaplotypeCallerGvcf_GATK4/5c9a1b93-7f39-424f-950e-70542e19e0b1/call-HaplotypeCaller/shard-5/HB3hg382.g.vcf.gz, command failed: CommandException: No URLs matched: /mnt/local-disk/HB3hg382.g.vcf.gz\nCommandException: 1 file/object could not be transferred.\n)"
Please help.
Thanks a lot.
Ming-yi