Open poddarharsh15 opened 2 months ago
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-"${BIN_VERSION}" \ bgzip -c > output/HG002_trio_merged.vcf.gz
udocker run \ -v "${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
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.gzError 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