GISAID sequences preprocess issue

[tushar-ahmed]

(base) d3w@d3w:~/covseq$ python3 preprocess/concatenate_fasta.py -i TRIAL/ -o TRIAL/test.fasta --gisaid_metadata gisaid_hcov19.xls
#########################

Concatenate all FASTA

#########################
Input: TRIAL/
Output: TRIAL/test.fasta
Traceback (most recent call last):
File "preprocess/concatenate_fasta.py", line 79, in
main()
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "preprocess/concatenate_fasta.py", line 74, in main
cngb_id_map = get_cngb_id_map(cgnb_metadata)
File "preprocess/concatenate_fasta.py", line 11, in get_cngb_id_map
with open(in_fn) as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType

I am facing this issue. help please

NB: I have installed python dependencies in conda environment.

[milw]

apparently you need to specify both --cngb_metadata and --gisaid_metadata