Unable to download fastq files in parallel / SOS

Unable to download fastq files in parallel / SOS

0

Hi!

Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language.

I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:

fastq-dump.2.10.9 err: error unexpected while resolving query within virtual file system module - No accession to process ( 500 )

Does anyone have any suggestions? I can download fastq files individually but for an upcoming experiment will have over 50 files so I need to be able to download parallel.

MORE INFO:

I am doing everything on an hpc cluster within the scratch directory. I have a directory named rnaseqtrial and within it I have the accession list. Once I switch to a computing node I simply run :

for i in $(cat /scratch/eag88/trial/SRR_Acc_List.txt ); do sbatch download.sh ${i}; done

download.sh :

#!/bin/bash
#SBATCH --job-name=download
#SBATCH --mail-type=ALL
#SBATCH --mail-user=my email
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem-per-cpu=4G

module load sra-tools/2.10.9
output_dir= “/scratch/eag88/rnaseqtrial /rawsamples"
mkdir -p $output_dir
fastq-dump —gzip —split-files $1 —outdir $output dir


slurm


rna-seq


bioinformatics


fastq


sequencing

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