Failure in annotate.py with lookup_taxonomy

[edwhisnant]

Hey,

I have been running into an issue with the annotate module. The jobs are failing after the MEROPS search during the busco proteome search with lookup_taxonomy() . What is weird is that there is no problem during the training module, when lookup_taxonomy was run to get the taxonomy for busco and augustus and was able to successfully extract this information.

I have been processing hundreds of genomes from across the Ascomycota and have only encountered this issue from MAGs from the Peltigerales (Lecanoromycetes). I was originally providing the --species using the genus_species name, which has generally worked fine. Instead of the genus_species name, I have tried to explicitly say "Lecanoromycetes" or "Ascomycota" to see if it was the genus name that was causing issues, but this did not resolve anything.

Example of the error output:

[...]

MEROPS search resulted in 202 hits and finished in 2.21 seconds�[0m
Traceback (most recent call last):
  File "/hpc/group/bio1/ewhisnant/miniconda3/envs/funannotate2/bin/funannotate2", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/hpc/group/bio1/ewhisnant/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/__main__.py", line 30, in main
    annotate(args)
  File "/hpc/group/bio1/ewhisnant/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/annotate.py", line 240, in annotate
    taxonomy = lookup_taxonomy(args.species)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/hpc/group/bio1/ewhisnant/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/utilities.py", line 336, in lookup_taxonomy
    if " " in name:
       ^^^^^^^^^^^
TypeError: argument of type 'NoneType' is not iterable
grep: /work/edw36/peltigerales/funannotate2/v25.09.29/peltigerales/Coccocarpia_palmicola_SRR14722230/annotate_results/Coccocarpia_palmicola_SRR14722230.fasta: No such file or directory
�[31m[ERRO]�[0m stat /work/edw36/peltigerales/funannotate2/v25.09.29/peltigerales/Coccocarpia_palmicola_SRR14722230/annotate_results/Coccocarpia_palmicola_SRR14722230.fasta: no such file or directory
�[31m[ERRO]�[0m stat /work/edw36/peltigerales/funannotate2/v25.09.29/peltigerales/Coccocarpia_palmicola_SRR14722230/annotate_results/Coccocarpia_palmicola_SRR14722230.fasta: no such file or directory

[nextgenusfs]

I think this is related to the fix in #30 as it is using same function, what I get now looks like this, which seems correct:

>>> from funannotate2.utilities import *
>>> tax = lookup_taxonomy("Coccocarpia palmicola")
>>> tax
{'superkingdom': 'Eukaryota', 'kingdom': 'Fungi', 'phylum': 'Ascomycota', 'class': 'Lecanoromycetes', 'order': 'Peltigerales', 'family': 'Coccocarpiaceae', 'genus': 'Coccocarpia', 'species': 'Coccocarpia palmicola'}
>>> choose_best_busco_species(tax)
'ascomycota'

[edwhisnant]

Hi again,

For some reason, I am continuing to run into this issue, exclusively with genomes from the Peltigerales. What is strange is that not all of them are running into this hiccup.

It seems almost arbitrary which ones fail and which ones do not, but when they do it always right after the MEROPS search, with the lookup_taxonomy function.

Would it help to provide the fasta files of one that failed and one that didnt?

[nextgenusfs]

Sure if you can point me to the assembly of one that works and then one that is failing and the commands you are running I can try to replicate locally (and hopefully fix it).