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philarevalo / PopCOGenT

Microbial Populations as Clusters Of Gene Transfer
GNU General Public License v3.0
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PopCOGenT run error #9

Open Diamonds95 opened 5 years ago

Diamonds95 commented 5 years ago

I had run PopCOGenT.sh successfully before, but when I use another dataset it failed, the error message is : Traceback (most recent call last): File "cluster.py", line 315, in main() File "cluster.py", line 70, in main linear_model=negative_selection_linear_fit()) File "cluster.py", line 298, in make_edgefile n2 = ','.join(clonal_components[n2]) TypeError: sequence item 0: expected str instance, numpy.int64 found Is there any special requirements for input fasta_file name?

philarevalo commented 5 years ago

Yes, I think this is an issue with the genome names being interpreted as integers and not strings. Do your genome filenames only have numbers (aside from the .fasta extension)?

I should be able to have a fix out for this, but unfortunately I probably won't be able to get to it for at least a week.

Diamonds95 commented 5 years ago

Thanks for your reply! Yes , all my fasta file were named by only numbers. Maybe I can rename them and try again!