Output not generated when filtered sequences

[DaniDelHoyo]

I have been experiencing some errors with the output of VaxignML when there are filtered sequences and I have noticed 2 bugs:

• When all the sequences are filtered (first I didn't realize they had to be >50 residues and tried smaller ones), the script just keeps running forever instead of showing any kind of error. I am not sure at what point it is getting stuck.
• When I introduced a couple of not recognized residues in one sequence, this sequence is filtered and everything proceeds correctly but then the output is not generated because of this error:

  final output... (<class 'KeyError'>, KeyError('XX',), <traceback object at 0x795473e31948>)

Seems like the not recognized residues are mistaken by a new sequence name at some point?

[abrozzi]

SPAAN is causing the issue. In lib/spaan/SPAAN/filter.c, you can see a comment indicating that proteins shorter than 50 amino acids are filtered out. Additionally, non-canonical amino acids are incompatible with PSORT.

My suggestion: write a script to sanitize your input FASTA file by removing sequences shorter than 50 amino acids and any sequences containing non-canonical amino acids.