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SegataLab / viromeqc

ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respect to the expected prokaryotic markers abundances in reference metagenomes
MIT License
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Can't detect LSU and SSU reads #8

Open shiraz-shah opened 1 year ago

shiraz-shah commented 1 year ago

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 "-".