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