MMSeqs-based Alignment Taking Very Long

[hnisonoff]

Hi, I am not sure if this is a bug or not but when I am using precompute_alignments_mmseqs.py to create an alignment for a single protein with ~300 amino acids it is taking ~24 minutes. The server this is running on has over 500G of RAM and 128 CPUs. I was under the impression that the mmseqs pipeline should be able to compute this alignment much faster. Do you have any guidance as to what is going on? Thanks!