Question: Help regarding fastq-dump
0
gravatar for govind.warier
3.4 years ago by
govind.warier0 wrote:

Hi,

I have been trying to convert a sra file to fastq and encountered following error message:

fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR2053277.sra

I've placed the fastq-dump executable file in the same folder as the sra file. I have used the following command

fastq-dump -A SRR2053277.sra

There are two fastq-dump executable files in the sra tollkit / bin such as fastq-dump.1.0.0 and fastq-dump.2.6.2. I have used both these names in place of 'fastq-dump' but got the error messages such as

fastq-dump.2.6.2: command not found

and

fastq-dump.1.0.0: command not found

How can I avoid getting these errors?

Please help...

Regards, Govind

software error • 3.5k views
ADD COMMENTlink modified 3.4 years ago by h.mon27k • written 3.4 years ago by govind.warier0

Is there anyone around you, who is familiar with Unix?

This looks like a path-type problem.

Don't move the fastq-dump folder. Leave it where it's installed. When you invoke fastq-dump, you need to enter the full path

/full/path/to/fastq-dump

For example, the full command on my machine looks like this:

/data/tools/sratoolkit.2.5.2-ubuntu64/bin/fastq-dump.2.5.2 SRRXXX.sra

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by jotan1.2k
0
gravatar for h.mon
3.4 years ago by
h.mon27k
Brazil
h.mon27k wrote:

(Assuming linux, which you do not state) Either:

./fastq-dump -A SRR2053277.sra

or

export PATH=/path/to/sratoolkit/bin:$PATH
fastq-dump -A SRR2053277.sra
ADD COMMENTlink written 3.4 years ago by h.mon27k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2417 users visited in the last hour