I am trying to screen my metagenomic libraries for antimicrobial peptides present. Therfore I downloaded the database from APD3 (https://academic.oup.com/nar/article/44/D1/D1087/2503090) (https://wangapd3.com/APD_sequence_release_09142020.fasta). After filtering peptides coming from bacteria only I tried to build markers using shortbred_identify.py against UniRef90.
However, I was not able to get any markers. After Grouping my input proteins with CD-HIT no sequences have been sorted. The input proteins are quite small (Min: 2, 25% Quartile 19, Median 30, 75% Quartile 44, Max 100 amino acids.
Do I need to adjust flags like --markerlength or --minAln (the minimum for a short, high-identity region.)? I played around with these flags but got only errors.