I have the Uniref90 dataset containing around 76M sequences. I have made modifications to all sequences based on a reduced amino acid alphabet.
I am trying to cluster it again at 90% identity. I am using
mmseq cluster on a 64 core, 500GB RAM machine. It has been more than 12h now.
Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 74390789 Target db start 1 to 74390789 [=
How long does it normally take to cluster such a database? I know I can use
linclust instead to cluster in linear time, but it might not be what I need in this case.
I am using
mmseq cluster as follows:
mmseqs createdb "uniref90-$1.fasta" "uniref90-DB-$1" mmseqs cluster "uniref90-DB-$1" "uniref90-DB-$1_clu" tmp/ --cov-mode 2 -c 0.8 --min-seq-id 0.9