Can't detect LSU and SSU reads

[shiraz-shah]

Hey SegataLab,
I've installed viromeqc but I'm experiencing the folling problems:

1. Getting the git repo doesn't download cmseq by default. One needs to get it manually and put it into the correct folder

2. LSU and SSU reads are not detected, skewing the enrichment score, making the enrichment score better than it is

3. Although viromeQC runs to completion, there's the following error in the output:

Traceback (most recent call last):
  File "/home/shiraz/apps/viromeqc/cmseq/cmseq/filter.py", line 5, in <module>
    from cmseq import __version__
ImportError: cannot import name '__version__' from 'cmseq' (/home/shiraz/apps/viromeqc/cmseq/cmseq/cmseq.py)
[main_samview] fail to read the header from "-".
Traceback (most recent call last):
  File "/home/shiraz/apps/viromeqc/cmseq/cmseq/filter.py", line 5, in <module>
    from cmseq import __version__
ImportError: cannot import name '__version__' from 'cmseq' (/home/shiraz/apps/viromeqc/cmseq/cmseq/cmseq.py)
[main_samview] fail to read the header from "-".