Hello,

I am trying to run DefenseFinder following the installation instructions from the GitHub repository, but I encounter the following error when running the tool.

Command used:

defense-finder run -o Salida2 -w 4 zcphages.n20.fasta

Output:

2026-03-16 13:01:33 | INFO | Received file zcphages.n20.fasta
2026-03-16 13:01:33 | INFO | zcphages.n20.fasta is a nucleotide fasta file. Prodigal will annotate the CDS

Traceback (most recent call last):
File "/home/pedrobarria/.conda/envs/defensefinder/bin/defense-finder", line 7, in
sys.exit(cli())
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/pedrobarria/.conda/envs/defensefinder/lib/python3.9/site-packages/defense_finder_cli/main.py", line 131, in run
sname = seq.name.decode()
AttributeError: 'str' object has no attribute 'decode'

Environment information:

• Installed using conda
• Python versions tested: 3.13, 3.10 and 3.9
• Same error occurs with all versions
• Input file: nucleotide FASTA (zcphages.n20.fasta)

I followed the installation instructions from the GitHub repository.

Do you know what might be causing this issue or how to fix it?

Thank you very much for your help.

Best regards,
Pedro