Hello,

I hope someone can help me out with an error trying to run Trimmomatic from within a bash script

This is the script:

#!/bin/bash 
FORWARD=$1 
REVERSE=$2 
trimmomatic PE -threads 72 $FORWARD $REVERSE paired_forward.fastq.gz unpaired_forward.fastq.gz paired_reverse.fastq.gz unpaired_reverse.fastq.gz ILLUMINACLIP:/opt/trimmomatic/adapters/NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
(all in one line)

When trying to run:

bash trim_script.sh example_forward.fastq.gz example_reverse.fastq.gz

I get error:

TrimmomaticPE: Started with arguments:
 paired_forward.fastq.gz paired_forward.fastq.gz paired_reverse.fastq.gz unpaired_reverse.fastq.gz ILLUMINACLIP:/opt/trimmomatic/adapters/NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
"xception in thread "main" java.lang.NumberFormatException: For input string: "36
        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
        at java.lang.Integer.parseInt(Integer.java:580)
        at java.lang.Integer.parseInt(Integer.java:615)
        at org.usadellab.trimmomatic.trim.MinLenTrimmer.<init>(MinLenTrimmer.java:11)
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:56)
        at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

There are no spaces or quotes in the MINLEN:36 step I have manually typed the line but I can't figure out why the error appears. Any help is much appreciated

EDIT: Corrected the repeated file.