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Failure while waiting for FeatureReader to initialize ?

ChipChip 415M 4053Member, Broadie

Hi

I've been trying to run joint-discovery-gatk4 on 304 normal WGS samples in batches of 15 using gatk/joint-discovery-gatk4Snapshot ID: 11 copied from workspace help-gatk/Germline-SNPs-Indels-GATK4-b37 . One batch of 15 persistently fails with a message from GenomicsDBImport:

A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///cromwell_root/fc-035f5652-acf7-4642-abb7-e8c10848c8ed/36e0b644-3aa3-4a01-8444-8f262b125154/HaplotypeCallerGvcf_GATK4/c097d279-8468-491b-b703-cd54b8d3c227/call-MergeGVCFs/REBC-ADJU-NT1-A-1-1-D-A526-36.g.vcf.gz

The file that can't be read seems to be fine:

$ gsutil ls -lah gs://fc-035f5652-acf7-4642-abb7-e8c10848c8ed/36e0b644-3aa3-4a01-8444-8f262b125154/HaplotypeCallerGvcf_GATK4/c097d279-8468-491b-b703-cd54b8d3c227/call-MergeGVCFs/REBC-ADJU-NT1-A-1-1-D-A526-36.g.vcf.gz
12.05 GiB 2018-09-11T21:05:35Z gs://fc-035f5652-acf7-4642-abb7-e8c10848c8ed/36e0b644-3aa3-4a01-8444-8f262b125154/HaplotypeCallerGvcf_GATK4/c097d279-8468-491b-b703-cd54b8d3c227/call-MergeGVCFs/REBC-ADJU-NT1-A-1-1-D-A526-36.g.vcf.gz#1536699935422867 metageneration=1
TOTAL: 1 objects, 12942143888 bytes (12.05 GiB)

Should I consider reducing the batch of 15 WGS g.vcfs to 10, increase the memory from 7GB , or
increase disk parameters for joint-discovery-gatk4 "huge_disk", "large_disk", "medium_disk", or "small_disk" ?

Answers

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