search

vibansal / HapCUT2

software tools for haplotype assembly from sequence data
BSD 2-Clause "Simplified" License
207 stars 36 forks source link

Segfault on extracthairs #115

Open klannert opened 3 years ago

klannert commented 3 years ago

I'm trying to run HapCUT2 on a single-sample VCF, not an especially large one (3184 variants). ExtractHAIRS chokes midway and gives a segfault:

reading sorted bamfile VWDSeq_215.bam processing reads mapped to chrom "chr1" processing reads mapped to chrom "chr2" cleaning buffer for prev chrom fragments 219 Segmentation fault: 11

Running this on MacOS 11.4.

vibansal commented 3 years ago

Which version of HapCUT2 are you using (it will help figure out if the problem is due to a recent change)? Also, does ExtractHAIRS work on other datasets that you may have analyzed? Thanks.

klannert commented 3 years ago

This install is v1.3.1, and this is my first time running this version on this OS. I have an older version working well on a machine with MacOS 10.14.7, I think that one is running HapCUT2 v1.2.