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Merging vcf files error with glnexus:v1.2.7 #312

@poddarharsh15

Description

@poddarharsh15

Describe the issue:
Merging vcf files error.
Setup

Operating system: working on cluster
DeepVariant version:latest
Installation method (Docker):
Type of data: (GIAB AshkenazimTrio [HG002,HG003,HG004] analysis.)
Steps to reproduce:

Command:
udocker run \ -v "${PWD}/output":"/output" \ quay.io/mlin/glnexus:v1.2.7 \ /usr/local/bin/glnexus_cli \ --config DeepVariant_unfiltered \ /output/HG002.g.vcf.gz \ /output/HG003.g.vcf.gz \ /output/HG004.g.vcf.gz \ | udocker run -i google/deepvariant:deeptrio-"${BIN_VERSION}" \ bcftools view - \ | udocker run -i google/deepvariant:deeptrio-"${BIN_VERSION}" \ bgzip -c > output/HG002_trio_merged.vcf.gz

Error trace: (if applicable)
Num BCF records read 118736378 query hits 14552613
[E::bgzf_read_block] Invalid BGZF header at offset 265038798
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read] Read block operation failed with error 3 after 0 of 32 bytes
Error: BCF read err

Screenshot from 2024-05-06 15-00-29

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