Cannot Generate Trimmomatic Output Files

Question

[matthew.sinton]

Hi All,

I'm trying to run a script on our university supercomputer, to use Trimmomatic to trim my paired end fastq files before I align them to my ref. genome. I was expecting to get similar outputs to those listed below:

filename.trim_1.fq.gz
filename.trim_2.fq.gz
filename.trim.unpaired_1.fq.gz
filename.trim.unpaired_2.fq.gz

However, I'm getting outputs like:

trimmomatic.po5224123

The script that I've been using is:

#!/bin/sh

# Grid Engine options (lines prefixed with #$)

#$ -N trimmomatic

#$ -cwd

#$ -l h_vmem=30G

#$ -pe sharedmem 2

# Initialise the environment modules

. /etc/profile.d/modules.sh

module load igmm/apps/trimmomatic/0.36 

java -jar trimmomatic-0.36.jar PE -phred33 FCHWCCKBBXX_L1_HKRDHUMosiOAAARAAPEI-209_1.fq.gz FCHWCCKBBXX_L1_HKRDHUMosiOAAARAAPEI-209_2.fq.gz Control1.trim_1.fq.gz Control1.trim.unpaired_1.fq.gz Control1.trim_2.fq.gz Control1.trim.unpaired_2.fq.gz ILLUMINACLIP:contaminants.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:26

java -jar trimmomatic-0.36.jar PE -phred33 FCHWCCKBBXX_L1_HKRDHUMosiOAABRAAPEI-210_1.fq.gz FCHWCCKBBXX_L1_HKRDHUMosiOAABRAAPEI-210_2.fq.gz Control2.trim_1.fq.gz Control2.trim.unpaired_1.fq.gz Control2.trim_2.fq.gz Control2.trim.unpaired_2.fq.gz ILLUMINACLIP:contaminants.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:26

I've been trying to see where I've gone wrong, and honestly can't. Any help would be greatly appreciated! Thanks!

[finswimmer]

Hello and welcome to biostars matthew.sinton ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[matthew.sinton]

Sorry, I was unaware of that. Thanks for doing that for me

[h.mon]

What is the content of "trimmomatic.po5224123"? Show us the output of:

cat trimmomatic.po5224123 | head