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Use the following PBS Pro submission script to fetch the FASTQ files for all listed samples. Note, data will be downloaded to the folder where the job is submitted. Example script (fetch_SraAccList.pbs).
Option 1:
| Code Block | ||
|---|---|---|
| ||
#!/bin/bash
#usage: ./fetch_SraAccList.sh SraAccList.txt
for r1 in `cat $1`;
do
qsub <<EOF
#!/bin/bash -l
#PBS -N $(basename $r1)
#PBS -l walltime=10:00:00
#PBS -l mem=8G
#PBS -l ncpus=4
cd $PBS_O_WORKDIR
#activate conda environment
conda activate sra
#fetch FASTQ files
prefetch $r1
fastq-dump --split-files $r1
EOF
done |
Option 2:
| Code Block | ||
|---|---|---|
| ||
#!/bin/bash #PBS -N SRA #PBS -l walltime=12:00:00 #PBS -l mem=8G #PBS -l ncpus=4 cd $PBS_O_WORKDIR #activate conda environment conda activate sra LIST='SraAccList.txt' #fetch FASTQ files for i in `cat $LIST`; do echo $i prefetch $i fastq-dump --split-files $i done |
Submit the job to the HPC cluster:
| Code Block | ||
|---|---|---|
| ||
./fetch_SraAccList.sh SraAccList.txt |
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