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bcftools produces seg fault with consensus command #1245

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JacobPorter opened this issue Jun 16, 2020 · 1 comment
Closed

bcftools produces seg fault with consensus command #1245

JacobPorter opened this issue Jun 16, 2020 · 1 comment

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@JacobPorter
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JacobPorter commented Jun 16, 2020

var.vcf.gz
1035377.4.fna.gz
var.vcf.gz.tbi.gz

  1. Fastq data from the SRA read archive was downloaded with accession SRR10961160.
  2. This data was aligned to the given Yersinia pestis genome with Bowtie2 2.2.9.
  3. FreeBayes v1.3.2-1-gabab37f was run on the alignment files.
  4. bcftools was used with the following command (with both versions 1.9 and 1.3):
    bcftools consensus -c chain -f 1035377.4.fna var.vcf.gz > consensus
  5. A segmentation fault was produced.

Attached are data files that were used to produce the result.
bgzip version 1.9 was used for var.vcf.gz

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