I'm Currently trying to do some Functional Annotation/Protein classification with InterProScan, particularly using the Pfam analysis. I input amino acid sequences from metagenomes that were hits on a previous blastp analysis. When running InterProScan, the analysis finish successfully, with no errors. Nonetheless, a very small subset of the total input were matches for InterProScan analysis. In addition, the output of these results show me that the matches were only related with ATPase, AAA-type, core; Pfam PF00004; GO:0005524; IPR003593 and IPR003959. Given that I'm working with metagenomic data, I was expecting to get a wide diversity in Pfam, GO and IPR. Do you have any idea what could be causing this? Does InterProScan need a reference database in addition to the ones it already has?
interproscan.sh -goterms -iprlookup -appl Pfam -i IntPro_input.txt -o IntPro_output.txt -f tsv
I'm running InterProScan v5 in standalone mode on Linux (interproscan-5.38-76)
