Question: Converting .sra files to fastq
0
gravatar for Linda
3.4 years ago by
Linda140
India
Linda140 wrote:

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?

fastq sra • 5.7k views
ADD COMMENTlink modified 3.4 years ago by piet1.4k • written 3.4 years ago by Linda140
1

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Zhaorong1.1k
1

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

ADD REPLYlink written 3.4 years ago by eddie.im130

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

ADD REPLYlink written 3.4 years ago by tangming20052.2k
3
gravatar for Varun Gupta
3.4 years ago by
Varun Gupta900
United States
Varun Gupta900 wrote:

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

ADD COMMENTlink written 3.4 years ago by Varun Gupta900

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?

ADD REPLYlink written 3.4 years ago by Linda140

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

 

ADD REPLYlink written 3.4 years ago by Linda140
0
gravatar for piet
3.4 years ago by
piet1.4k
planet earth
piet1.4k wrote:

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

 

ADD COMMENTlink written 3.4 years ago by piet1.4k
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