Converting .sra files to fastq

Question

[Linda]

I am trying to convert .sra files to fastq using fastq-dump on a CentOS machine. I already have the sra files downloaded so I do not want to redownload them. The command sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR554454.sra seems to do nothing. There is no error, no output, and it does not seem to be using up any cpu or network either. What am I doing wrong?

[Zhaorong]

You are using the correct command. This link says "fastq-dump would still attempt to contact NCBI to obtain the references needed to convert the data to fastq". So is it possible that there is a network connection problem? I would suggest using a small dataset first, since the process takes a while. And also try to do fastq-dump SRR554454 directly, which download the data from SRA and then output the data in fastq format.

[eddie.im]

It's important to use the --split-files if it is paired end, otherwise you will get a very messy fastq file

[Ming Tommy Tang]

You sure the sra file is in the same directory as you invoke fastq-dump?

Answer 1

[Varun Gupta]

HI,

I just downloaded the file and used this and it worked

/apps1/sratoolkit/2.3.3-2/bin/fastq-dump --split-files SRR554454.sra

2 separate files are produced (paired end) SRR554454_1.fastq SRR554454_2.fastq

[Linda]

This does nothing in my case, as before, no activity at all, or error. Does this try to connect to ncbi even if the sra file is downloaded?

[Linda]

Apparently it does need to connect to ncbi. Once I moved to a machine outside the firewall, it worked fine.

Answer 2

[piet]

According to this recipe I used option -A to convert a file which I had already downloaded locally. For debugging it may also help to set option -v once or several times.

fastq-dump -v -A ./SRR554454.sra