Converting sra to fastq
1
1
Entering edit mode
8.5 years ago
sagardesai91 ▴ 50

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!

RNA-Seq • 3.7k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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!

ADD REPLY
1
Entering edit mode

Add sratoolkit to environment variables

export PATH=$PATH:/path/to/sratoolkit/bin/
fastq-dump --split-3 filename.sra
ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

The command is as follows:

fastq-dump <sra_file>
ADD REPLY
2
Entering edit mode
ADD COMMENT
0
Entering edit mode

Haha! I ended up doing that itself. Thanks!

ADD REPLY

Login before adding your answer.

Traffic: 3131 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6