When using pysam.bcftools.mpileup, I keep getting an error that says: "Segmentation fault (core dumped)". Other commands seem to work fine (e.g. pysam.bcftools.call). Here's a simple example for reproducibility:
[sbslee@grc141 20200613_pysam_test]$ cat pysam-bcftools-mpileup-issue.py import pysam.bcftools pysam.bcftools.mpileup() [sbslee@grc141 20200613_pysam_test]$ python3 pysam-bcftools-mpileup-issue.py Segmentation fault (core dumped)
As you can see, the error occurs even without any arguments to the function call, which suggests there might be a bug. Does anyone have an idea for why this is happening? Please note that I already posted a couple of issues related to this on the GitHub repository for pysam (#928 and #944).
-I downloaded pysam through pip.
-Below is information about the machine I'm using.
[sbslee@grc141 20200613_pysam_test]$ uname -a Linux grc141.grid.gs.washington.edu 2.6.32-754.28.1.el6.x86_64 #1 SMP Wed Mar 11 18:38:45 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
-Below is information about the pysam version I'm using.
[sbslee@grc141 20200613_pysam_test]$ cat /nfs/home/sbslee/.local/lib/python3.6/site-packages/pysam/version.py # pysam versioning information __version__ = "0.16.0" __samtools_version__ = "1.10" __bcftools_version__ = "1.10.2" __htslib_version__ = "1.10.2"