Error running PhaTYP

[lingrongjin]

I ran into an error when trying to run PhaTYP to predict viral lifestyles and would like some help for debugging.
Here is the code I used:
phabox2 --task phatyp
--dbdir Database/__MACOSX/phabox_db_v2
--outpth phatyp_out
--contigs viral_contigs.fasta
--len 5000 \

And the error I got:
Running program: PhaTYP (Lifestyle prediction)
[1/7] filtering the length of contigs...
[2/7] calling genes with prodigal...
running with cpu
Traceback (most recent call last):
File "Software/miniconda3/envs/phabox2/bin/phabox2", line 10, in
sys.exit(main())
^^^^^^
File "Software/miniconda3/envs/phabox2/lib/python3.12/site-packages/phabox2/phabox2.py", line 408, in main
phatyp.run(inputs)
File "Software/miniconda3/envs/phabox2/lib/python3.12/site-packages/phabox2/phatyp.py", line 122, in run
parallel_prodigal_gv(f'{rootpth}/filtered_contigs.fa', f'{rootpth}/{midfolder}/query_protein.fa', threads)
File "Software/miniconda3/envs/phabox2/lib/python3.12/site-packages/phabox2/scripts/parallel_prodigal_gv.py", line 100, in main
append_fasta_file(
File "Software/miniconda3/envs/phabox2/lib/python3.12/site-packages/phabox2/scripts/parallel_prodigal_gv.py", line 42, in append_fasta_file
match.group(1)
^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'group'

[KennthShang]

Hi @lingrongjin ,

It seems it is an issue thrown by the prodigal-gv. You can try to translate your contigs into protein (using either prodigal or prodigal-gv) first. Then, using the following codes to run phabox2:

phabox2 --task phatyp
--dbdir Database/__MACOSX/phabox_db_v2
--outpth phatyp_out
--contigs viral_contigs.fasta
--proteins [your protein file]
--len 5000

If the size of your viral_contigs.fasta is less than 200Mb, then you can also do a quick check via our webserver: https://phage.ee.cityu.edu.hk/. If the webserver gives an error, this means some thing wrong with your FASTA. In this case, maybe some special characters exist in your FASTA I suppose.

Best,
Jiayu