Hello everyone,

I am running KOfam analysis on multiple files using the following script. However the process is slow. Is there a way I can speed up the run using GNU-parallel. I have never used GNU-parallel before. My script until now looks like this

#!/bin/sh
source /opt/asn/etc/asn-bash-profiles-special/modules.sh

#load the module
module load kofamscan/1.3.0

#make a forloop with the isolate names
ls *_accessory_proteins.fasta | sed 's/_.*$//' > file_list1.txt

files=`cat file_list1.txt`

for  var in $files
do
echo $var

exec_annotation --cpu=15 -E 0.01 --tmp-dir=${var} -p /apps/bio/unzipped/kofam/profiles -k /apps/bio/unzipped/kofam/ko_list -f mapper -o ${var}_accessory_KOfam.txt ${var}_accessory_proteins.fasta

done

Thanks!!