bowmanjeffs
commented
9 months ago Thanks for letting me know. It looks like a few things are going on. First, esl-alimerge isn't in your path. Second, there seems to be a further issue with the call to cmalign, which might clear up once the path issue is fixed. Let me know if it still gives you trouble. I do recommend installing all dependencies as you're doing but if need be you could also consider using the Docker image.
Dear Jeff,
I am facing some problems with running the line: ./paprica-run.sh test bacteria
This is the error message produced: Incorrect number of command line arguments. Usage: cmalign [-options]
where basic options are: -h : show brief help on version and usage -o : output the alignment to file , not stdout
-g : configure CM for global alignment [default: local]
To see more help on available options, do cmalign -h
/bin/bash: line 1: esl-alimerge: command not found Traceback (most recent call last): File "/mnt/c/Program Files/WSL/paprica/paprica-place_it.py", line 1323, in
split_query_ref(cwd + query + '.clean.unique.align.sto',
File "/mnt/c/Program Files/WSL/paprica/paprica-place_it.py", line 282, in split_query_ref
for record in SeqIO.parse(query_alignment, 'stockholm'):
File "/home/angelwyc/anaconda3/envs/paprica_env/lib/python3.10/site-packages/Bio/SeqIO/init.py", line 608, in
return (r for alignment in AlignIO.parse(handle, format) for r in alignment)
File "/home/angelwyc/anaconda3/envs/paprica_env/lib/python3.10/site-packages/Bio/AlignIO/init.py", line 322, in parse
with as_handle(handle) as fp:
File "/home/angelwyc/anaconda3/envs/paprica_env/lib/python3.10/contextlib.py", line 135, in enter
return next(self.gen)
File "/home/angelwyc/anaconda3/envs/paprica_env/lib/python3.10/site-packages/Bio/File.py", line 72, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: '/home/angelwyc/paprica/test.bacteria.clean.unique.align.sto'