search

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
Other
675 stars 240 forks source link

bcftools call -A => segmentation fault #2224

Open bcantarel opened 4 months ago

bcantarel commented 4 months ago

I am running into a segmentation fault with bcftools call -A Similar to what was seen here: https://github.com/samtools/bcftools/issues/2118

with root@4cbb88ec94f0:/data# bcftools --version bcftools 1.20 Using htslib 1.20 Copyright (C) 2024 Genome Research Ltd. License Expat: The MIT/Expat license This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

Error: bcftools call -A --threads 8 -g 3 -mO z -o test.sambcf.g.vcf.gz test.mpileup Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Segmentation fault (core dumped)

Create Correct output: /usr/local/bin/bcftools call --threads 8 -g 3 -mO z -o test.sambcf.g.vcf.gz test.mpileup Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

pd3 commented 3 months ago

Thank you for the issue. Is there any chance you could provide a small test case to reproduce the error?

bcantarel commented 3 months ago

Unfortunately, I cannot share this sensitive customer data, but I generated the BAM using Giraffe with a pangenome that I created using Cactus-Minigraph.

pd3 commented 3 months ago

Any chances you could send the debugging output from valgrind?

pd3 commented 3 months ago

Could you perhaps use this script to create a small slice of the bam and the reference https://github.com/pd3/mpileup-tests/blob/main/misc/create-bam-test, as in #2189? The script creates a short artificial chromosome, removes all sample information, and anonymizes the data so that all A,C,G,T bases are randomly shuffled, so that the source region cannot be identified.