gistfile1.txt

#!/usr/bin/perl
use strict;
use warnings;

open IN, '<', "readlist.txt";
while (<IN>) {
    my ($left, $prefix) = split /\s+/, $_;
    open OUT, '>', "$prefix.trim.sh";
    print OUT "java -jar /usr/local/trimmomatic/latest/trimmomatic-0.32.jar SE -phred33 -threads 2 $left $prefix\.clean.fq.gz ILLUMINACLIP:/usr/local/trimmomatic/latest/adapters/TruSeq2-PE.fa:2:30:10 LEADING:10 TRAILING:10 MINLEN:50";
    system "qsub -q rcc-30d -pe thread 2 $prefix.trim.sh";
}