Trimmomatic 0.39 Permission denied accessing fastq.gz

Hello everyone,

I am still relatively new to bioinformatics and RNA-seq analysis so I apologise in advance if I haven’t provided enough/relevant information. I am trying to run trimmomatic as an array job. I have done this before for STAR and it worked so have used a very similar format as it worked previously. When I run the following script…

#!/bin/bash
#
#$ -cwd
#
#$ -V
#$ -l h_vmem=8G
#$ -l h_rt=47:59:59
#
# Task range. Tasks need to go from 1 to the number of files:
#$ -t 1-417


#load modules
module load igmm/apps/trimmomatic/0.39


# SGE_TASK_ID will go from 1 to the number of files when we submit an array job
sample_name=`sed -n ${SGE_TASK_ID}p < filename_list.txt`
echo Processing sample: ${sample_name} on $HOSTNAME


trimmomatic PE 
-threads 4 
-phred33 
-trimlog ./trimmed/trimmomatic_log.txt  
./ipads_rna/${sample_name}_1.fastq.gz ./ipads_rna/${sample_name}_2.fastq.gz 
./trimmed/${sample_name}.trimmed_1.fastq.gz ./trimmed/${sample_name}.un.trimmed_1.fastq.gz 
./trimmed/${sample_name}.trimmed_2.fastq.gz ./trimmed/${sample_name}.un.trimmed_2.fastq.gz 
ILLUMINACLIP:/home/s2126362/scratch/trimmomatic-0.39/adapters/TruSeq3-PE-2.fa/:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50

I get this output…

[scratch]$ cat trimmomatic.sh.e13708195.34
Usage:
   PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-
basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or:
   SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
or:
   -version
/var/spool/gridheduler/exed/node7d01/job_scripts/13705: line 26: ./ipads_rna/WTCHG_780324_70345010_1.fastq.gz: Permission denied

I cannot work out why I get the permission denied error message when it is run as an array job but not as a single command.

I have tried running the command on its own in the command line with a specific filename and it works perfectly and generates the 4 trimmed output files.

Any thoughts?

Thank you!