setup PFAM:

cd /workspace/meren/PFAM/
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gzip -d Pfam-A.hmm.gz
hmmpress Pfam-A.hmm

run like this:

time hmmscan --cpu 20 -o /dev/null --cut_ga --domtblout aa_sequences_01.pfam /workspace/meren/PFAM/Pfam-A.hmm aa_sequences_01.fa
time hmmscan --cpu 20 -o /dev/null --cut_ga --domtblout aa_sequences_02.pfam /workspace/meren/PFAM/Pfam-A.hmm aa_sequences_02.fa
time hmmscan --cpu 20 -o /dev/null --cut_ga --domtblout aa_sequences_03.pfam /workspace/meren/PFAM/Pfam-A.hmm aa_sequences_03.fa
