Hi Edna,
Thank you so much for making available your pipeline for metagenomics. It has helped me a lot. I am trying to use the cogformat.py for my resutls of rpsblast cog. However, it appears this error:

Traceback (most recent call last):
File "cogformat.py", line 60, in
output = formatCOG(directoryCOG)
File "cogformat.py", line 34, in formatCOG
COGinput = pd.read_csv(COGfiles[file2], sep='\s+', index_col = 0, names = ['Function', 'Count'])
File "/home/p277936/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 605, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/p277936/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 463, in _read
return parser.read(nrows)
File "/home/p277936/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 1052, in read
index, columns, col_dict = self._engine.read(nrows)
File "/home/p277936/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 2096, in read
values = data.pop(self.index_col[i])
IndexError: list index out of range

The line 2096 looks fine in the cog_stats.txt file (similar to the other lines). I am wondering if you have a suggestion to solve this issue.
Cheers,
Ed