How to run a batch .sra to .fastq processing loop using linux bash?

Question

[vassialk]

How to run a batch .sra to .fastq processing loop using linux bash and sratoolkit?

I am trying to run a script in a bin folder of sra tools:

#!/bin/bash
for I in `*.sra`;
do
    ./fastq-dump
done

[andrew.j.skelton73]

I imagine you're missing the $I at the end of ./fastq-dump, but either way, this is best suited to stack overflow

[vassialk]

stackoverflow sends to Biostars!!!

Answer 1

[Antonio R. Franco]

It will be a lot better to use parallel since it can do the work using all of the cores available in your computer at once, saving time

sudo apt-get install parallel  #Will install parallel if necessary
find *sra | parallel 'fastq-dump --split-3 {}'

An alternative that uses a different directory, 6 cores and a regular (not a legacy) extraction of the sra files

cat ../extdata/sraFiles.txt | parallel -j 6 fastq-dump -I --split-files ../sra/{}.sra

Answer 2

[dariober]

You should remove backticks (`...`) for your code to work. If your have more than 1 processor available, you might want to run fastq-dump in parallel with xargs. For example, run up to 5 processes in parallel:

ls *.sra | xargs -I {} -P 5 -n 1 ./fastq-dump {}

Answer 3

[Chirag Nepal]

for i in ls (*.sra)
do
    ./fastq-dump $i
done

Try this.

[elvissober]

Thank you, folks, how clever you are!!!

[Michael Dondrup]

So you are vassialk ? xD

[andrew.j.skelton73]

New User..... From South Africa this time...