Wrong in Step 4/5

[Niohuruzh]

Hi,
When I use the default program, I encounter an error:

Step 1/5: Conducting all-to-all comparisons.
          Completed!      

Step 2/5: Determining edge thresholds
          Completed!      

Step 3/5: Identifying network edges
          Completed!      

Step 4/5: Conducting clustering
Traceback (most recent call last):
  File "/home/leigod/anaconda3/envs/orthofinder/bin/orthohmm", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/leigod/anaconda3/envs/orthofinder/lib/python3.12/site-packages/orthohmm/orthohmm.py", line 182, in main
    execute(**process_args(args))
  File "/home/leigod/anaconda3/envs/orthofinder/lib/python3.12/site-packages/orthohmm/orthohmm.py", line 141, in execute
    generate_orthogroup_clusters_file(
  File "/home/leigod/anaconda3/envs/orthofinder/lib/python3.12/site-packages/orthohmm/helpers.py", line 578, in generate_orthogroup_clusters_file
    get_orthogroup_information(
  File "/home/leigod/anaconda3/envs/orthofinder/lib/python3.12/site-packages/orthohmm/helpers.py", line 525, in get_orthogroup_information
    lines = [entries[row["spp"]][row["name"]][i:i+70] for i in range(0, len(entries[row["spp"]][row["name"]]), 70)]
                                                                            ~~~~~~~^^^^^^^^^^^^
KeyError: np.str_('proteolyticus_proteolyticus.proteins.f')

I noticed that the file name proteolyticus_proteolyticus.proteins.f appears to be incorrect. It should be proteolyticus_proteolyticus.proteins.fa in my fasta files directory. Do you have any suggestions on how to address this issue?

Looking forward to your reply
Best wishes!

[JLSteenwyk]

Hi,

Thank you so much for writing and letting us know about this issue!

Do you have some of the input files you used so that I can reproduce this error and debug from there?

Cheers,

Jacob