Help with genes error: libchtslib

[elhwashington]

Hello,
I have been trying to get MIDAS, installed by a former lab member, to run. So far I think that I have run_midas.py species running but when I then try run_midas.py genes on the samples I just ran through species I receive the following error
Traceback (most recent call last):
File "/Users/mcleanlab/Tools/MIDAS/scripts/run_midas.py", line 757, in
run_program(program, args)
File "/Users/mcleanlab/Tools/MIDAS/scripts/run_midas.py", line 79, in run_program
genes.run_pipeline(args)
File "/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py", line 286, in run_pipeline
pangenome_coverage(args, species, genes)
File "/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py", line 149, in pangenome_coverage
count_mapped_bp(args, species, genes)
File "/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py", line 173, in count_mapped_bp
import pysam
File "/Users/mcleanlab/Downloads/pysam-master/pysam/init.py", line 5, in
from pysam.libchtslib import *
ImportError: No module named libchtslib
I have looked for libchtslib and found libchtslib.pxd, libchstlib.c and libchtslib.o deep inside the pysam-master folder. However, even adding the corresponding folders to the python path did not correct the issue.
I am looking for help. Hopefully I'm just confused and the answer is simple.

thank you for your time
Erik Hendrickson

[snayfach]

Please download the latest version of the code and run the testing code MIDAS/test/test_midas.py. This should let you know what the issue is, but I suspect it is related to your installed version of pysam.

Thanks,
Stephen

[elhwashington]

Thank you for the help. Sadly, I am on a legacy system and re-installing something is pretty much out. Fortunately, I have gotten the Docker version to run. Again, thank you for the reply Erik Hendrickson

…

On Sun, 26 Nov 2017, Stephen Nayfach wrote: Please download the latest version of the code and run the testing code MIDAS/test/test_midas.py. This should let you know what the issue is, but I suspect it is related to your installed version of pysam. Thanks, Stephen — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.[Af4lVWtOoJGG5F_pDRoZbRePb1Qoz6qeks5s6aMRgaJpZM4QcgZT.gif]

[snayfach]

In that case I'm closing this issue, but feel free to reopen as necessary.

Thanks,
Stephen

[nick-youngblut]

At least on some linux systems, the midas bioconda recipe is installing pysam=0.15.4, which when imported generates the ImportError: No module named libchtslib error. Specifyingpysam>=0.16 in the midas bioconda recipe should help to avoid the issue