...
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wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001000/SRR1039511SRR1039510/SRR1039511SRR1039510_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003000/SRR1039513SRR1039510/SRR1039513SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001000/SRR1039521SRR1039520/SRR1039521SRR1039520_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002001/SRR1039512SRR1039511/SRR1039512SRR1039511_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000001/SRR1039510SRR1039511/SRR1039510SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008001/SRR1039508SRR1039521/SRR1039508SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002001/SRR1039522SRR1039521/SRR1039522SRR1039521_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003004/SRR1039523SRR1039514/SRR1039523SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008004/SRR1039518SRR1039514/SRR1039518SRR1039514_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003007/SRR1039523SRR1039517/SRR1039523SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009008/SRR1039519SRR1039508/SRR1039519SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009008/SRR1039509SRR1039518/SRR1039509SRR1039518_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000008/SRR1039520SRR1039518/SRR1039520SRR1039518_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003/SRR1039513/SRR1039513_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002/SRR1039522/SRR1039522_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002/SRR1039512/SRR1039512_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/006/SRR1039516/SRR1039516_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/005/SRR1039515/SRR1039515SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/005/SRR1039515/SRR1039515_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/006009/SRR1039516SRR1039519/SRR1039516_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007009/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518SRR1039519/SRR1039519_2.fastq.gz |
Now create a PBS Pro submission script for the above and save it in a file called, for example ‘launch_ENA_download.pbs’. Note: the below script will download the data in the folder from where the script has been sent to the cluster.
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#!/bin/bash -l #PBS -N download #PBS -l select=1:ncpus=2:mem=8gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001000/SRR1039511SRR1039510/SRR1039511SRR1039510_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003000/SRR1039513SRR1039510/SRR1039513SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001000/SRR1039521SRR1039520/SRR1039521SRR1039520_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002001/SRR1039512SRR1039511/SRR1039512SRR1039511_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000001/SRR1039510SRR1039511/SRR1039510SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008001/SRR1039508SRR1039521/SRR1039508SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002001/SRR1039522SRR1039521/SRR1039522SRR1039521_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003004/SRR1039523SRR1039514/SRR1039523SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008004/SRR1039518SRR1039514/SRR1039518SRR1039514_12.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003007/SRR1039523SRR1039517/SRR1039523SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009008/SRR1039519SRR1039508/SRR1039519SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009008/SRR1039509SRR1039518/SRR1039509SRR1039518_21.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000008/SRR1039520SRR1039518/SRR1039520SRR1039518_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/003/SRR1039513/SRR1039513_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002/SRR1039522/SRR1039522_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/002/SRR1039512/SRR1039512_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/006/SRR1039516/SRR1039516_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/005/SRR1039515/SRR1039515SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/005/SRR1039515/SRR1039515_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/006009/SRR1039516SRR1039519/SRR1039516_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007009/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518SRR1039519/SRR1039519_2.fastq.gz |
Submit the download script to the cluster:
...