Help regarding fastq-dump

Question

[govind.warier]

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

[jotan]

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

Answer 1

[h.mon]

(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