Converting sra to fastq

Question

[sagardesai91]

Hello everyone,

I am trying to convert this set of sra files into the fastq format with the latest version of sratoolkit 2.5.4.1.

But I am getting an error which says the following:

fastq-dump.2.5.2 err: connection busy while validating within network system module - failed ERR375895.sra.

Could anyone please tell me how to resolve this? It would be of great help!

[Jon]

Have you downloaded the SRA file, or are you downloading it on the fly via sra-toolkit? Maybe fastq-dump is trying to download it but has not been properly configured for downloading. Configuring instructions here: https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration

[sagardesai91]

I have already downloaded the sra file and converting it on the terminal. I am doing this job on a cluster, and when I run the config file, it gives me a system look up error!

[Karma]

Add sratoolkit to environment variables

export PATH=$PATH:/path/to/sratoolkit/bin/
fastq-dump --split-3 filename.sra

[george.ry]

And what is the exact command that you're using?

[sagardesai91]

The command is as follows:

fastq-dump <sra_file>

Answer 1

[GenoMax]

Just get the fastq from EBI: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR375/ERR375895/ERR375895.fastq.gz

[sagardesai91]

Haha! I ended up doing that itself. Thanks!