submit-wgetSRAFastqdump.sh

#!/bin/bash

#SBATCH --ntasks=8
#SBATCH --time=100:15:00
#SBATCH --mem=8048
#SBATCH --array=1-219%5
#SBATCH --output=fastqDumper%A_%a.out
#SBATCH --partition=primary

echo "SLURM_JOBID: " $SLURM_JOBID
echo "SLURM_ARRAY_TASK_ID: " $SLURM_ARRAY_TASK_ID
echo "SLURM_ARRAY_JOB_ID: " $SLURM_ARRAY_JOB_ID

scc=$(cat SRR_Acc_List_hinch.txt | sed -n ${SLURM_ARRAY_TASK_ID}"p")

echo $scc

mkdir data/$scc

wget --output-document=${scc}/${scc}.sra https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/${scc}/${scc}.1

mv ${scc}/${scc}.sra ${scc}/${scc}

fasterq-dump --split-files --outdir data/${scc}/ --threads 8 ${scc}/${scc}