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salzberg-lab / bolotie

SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
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Error running run.py #1

Closed luangasparclemente closed 2 years ago

luangasparclemente commented 3 years ago

I got this error when I tried to run. (args used --input --reference --outdir)

can not perform indexing, path finding, parents finding and plotting without provided clusters. You can use consensus calls to generate a tree and clusters Running stages: clean, align, consensus

================== Cleaning sequence names in all inputs Traceback (most recent call last): File "/"DELETED"/run.py", line 761, in main(sys.argv[1:]) File "/"DELETED"/run.py", line 757, in main args.func(args) File "/"DELETED"/run.py", line 666, in wrapper clean(args) File "DELETED"/run.py", line 307, in clean with open(args.clusters,"r") as inFP: TypeError: expected str, bytes or os.PathLike object, not NoneType

Any suggestions on how to resolve this issue?

Thanks!

cpockrandt commented 3 years ago

Hi @luangasparclemente,

thanks for trying it out and sorry for the late reply.

It seems that you have not passed clusters to the script. Bolotie requires you to have pre-assigned clusters for all the sequences to run. If you have any other questions, let us know.