Hi!
I'm trying to map multiple sra files (>6500) with bowtie2 against my reference genome. I am running slurm script in a server. While mapping for single sequence is working fine but when running bash loop all the time getting the following error
"path/to/slurm_script: line 16: path/to/file1.fastq: Permission denied"
Here is my slurm script
#!/bin/bash
#BATCH --job-name=ERR1135336.clean.reads.Assembly
#SBATCH -N 1 # Number of nodes, not cores
#SBATCH -t 2-00:00:00 # Walltime
#SBATCH --ntasks-per-node 40 # Number of cores
#SBATCH --output=out-%j.log # Output (console)
#SBATCH --partition=test # Queue
module use /gpfs/shared/modulefiles_local
module use /gpfs/shared/modulefiles_local/bio
module load bio/bowtie2/2.3.4
for i in $(path/to/*.fastq)
do
bowtie2 -x PC_805 --threads 40 -U ${i} -S path/to/${i%%.fastq}.sam
done
I am not sure whether this is really a permission issue or bash scripting issue.
Output of ls -l for the directory from where I am running slurm job
drwxr-xr-x 2 chayan.roy domain users 4096 Apr 23 10:14 PC_805
Output of ls -l for the directory where I am storing my fastq is
drwxr-xr-x 22 chayan.roy domain users 4096 Apr 22 14:44 HMP_2017
Any help will be much appreciated
Thanks
I'm trying to map multiple sra files (>6500) with bowtie2 against my reference genome. I am running slurm script in a server. While mapping for single sequence is working fine but when running bash loop all the time getting the following error
"path/to/slurm_script: line 16: path/to/file1.fastq: Permission denied"
Here is my slurm script
#!/bin/bash
#BATCH --job-name=ERR1135336.clean.reads.Assembly
#SBATCH -N 1 # Number of nodes, not cores
#SBATCH -t 2-00:00:00 # Walltime
#SBATCH --ntasks-per-node 40 # Number of cores
#SBATCH --output=out-%j.log # Output (console)
#SBATCH --partition=test # Queue
module use /gpfs/shared/modulefiles_local
module use /gpfs/shared/modulefiles_local/bio
module load bio/bowtie2/2.3.4
for i in $(path/to/*.fastq)
do
bowtie2 -x PC_805 --threads 40 -U ${i} -S path/to/${i%%.fastq}.sam
done
I am not sure whether this is really a permission issue or bash scripting issue.
Output of ls -l for the directory from where I am running slurm job
drwxr-xr-x 2 chayan.roy domain users 4096 Apr 23 10:14 PC_805
Output of ls -l for the directory where I am storing my fastq is
drwxr-xr-x 22 chayan.roy domain users 4096 Apr 22 14:44 HMP_2017
Any help will be much appreciated
Thanks
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