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luntergroup / octopus

Bayesian haplotype-based mutation calling

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Segmentation fault when running Cell command

chenv3 opened this issue · comments

commented

Describe the bug
Segmentation faults occurs when running the Cell command

Version

$ octopus --version
octopus version 0.7.4 (HEAD ed012a6)
Target: x86_64 Linux 3.10.0-862.14.4.el7.x86_64
SIMD extension: SSE2
Compiler: GNU 10.2.0
Boost: 1_78

Command line to run octopus:

$ octopus --working-directory worker --temp-directory-prefix temp -C cell -R genome.fa -I sample_alignments.bam -o sample.vcf --threads 12 -T chromosome_chunk

This segmentation fault occurs with and without the use of the regions flag. Supplying the regions flag and splitting the chromosomes into chunks has allowed a majority of the jobs to complete. Some of the jobs that had a segmentation fault were able to run to completion when restarted.

  • Reference hg38
  • 10x Cell Ranger generated BAM files used