Your path is hardcoded in a function you created

[stavnaky1]

Hi,
In bam_readcount.py, in this line:

os.system('/home/mnguyen/bam-readcount/bin/bam-readcount -i -w 0 -l {0} -f {1} '
'{2} > {3}'.format(sites_file_path, self.ref_file,
self.bam,
tumor_readcount_file_path))

You used a hard-coded path that matches your computer so it didn't work for me.
I fixed it on my own (just removing the whole path preceeding it),
but you should fix it as well in the environment.

Best,
Stav Naky