#! /usr/bin/env bash
mkdir -p cds_aln
echo -n > pal2nal.cmds
for i in pep_aln/*.pal; do
    j=$(basename "$i")
    echo "pal2nal.pl $i raw_ogs/cds/${j/.pal/.fa} -output fasta > cds_aln/${j/.pal/.nal}" >> pal2nal.cmds
done
xargs -t -P 8 -I cmd -a pal2nal.cmds bash -c "cmd"