#! /usr/bin/env bash
mkdir -p pep_aln
echo -n > mafft.cmds
for i in raw_ogs/pep/*.fa; do
    j=$(basename "$i")
    echo "linsi --quiet $i > pep_aln/${j/.fa/.pal}" >> mafft.cmds
done
xargs -t -P 8 -I cmd -a mafft.cmds bash -c "cmd"