GATK JointCalling doesn't allow for requester pay buckets Answered
GATK4-Germline-Preprocessing-VariantCalling-JointCalling Module 04 1-4-JointGenotyping-HG38 (github.com/broadinstitute/warp/JointGenotyping:JointGenotyping_v1.5.1) doesn't have a requester pay boolean option in its input and gives the following error:
Task JointGenotyping.ImportGVCFs:0:1 failed. Job exit code 2. Check gs://fc-81abf433-f373-4cdf-b3e8-1a699e73dd4c/bd1c881c-fcf0-4537-af28-b101175a4039/JointGenotyping/ce45d2ea-abcf-4878-82ff-2b6b6bae6cd4/call-ImportGVCFs/shard-0/stderr for more information. PAPI error code 9.
stderr:
*********************************************************************** A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: com.google.cloud.storage.StorageException: Bucket is requester pays bucket but no user project provided. ***********************************************************************
Comments
1 comment
Hi Stephanie,
Thanks for writing in. You can use this publicly available version of the JointGenotyping workflow that includes the option to include a requester pays project until the WARP team includes the option in their Dockstore workflow: https://portal.firecloud.org/#methods/jcerrato/JointGenotyping_v1.5.1_RPbuckets/2
Kind regards,
Jason
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