!/bin/bash

DIR=/users/prm0080/RepeatMasker/RepeatMasker/HMP_Bacteria_ContigCombine2
J=0
K=1
for i in $DIR/*
do
files[$J]=$i
let J=$J+$K
done

BSUB -J "jobArray[1-560]"

BSUB -n 1

BSUB -M 2

BSUB -e mothur.%J.err output error file; %J=job number

$LSB_JOBINDEX

Run the application

/users/prm0080/RepeatMasker/RepeatMasker/RepeatMasker ${files[$LSB_JOBINDEX]} -dir $DIR/suresh/