Error on pysam.bcftools.mpileup: "Segmentation fault (core dumped)"

Question

[sbstevenlee]

Hi,

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).

Notes:

-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"

Answer 1

[sbstevenlee]

Answering my own question: The pysam team responded to my Github issues! They said it was indeed a bug in pysam due to the fact that both bcftools and samtools have the ‘mpileup’ command. They are in the process of fixing the bug. See my Github issue for more details: https://github.com/pysam-developers/pysam/issues/928