Question: Erro while converting .SRA File to .fastq File with SRA Toolkit
0
gravatar for Cherry
4.0 years ago by
Cherry50
Germany
Cherry50 wrote:

Hi, everyone,

I have download 6 paired end sequencing data from Ncib, and I am trying to convert them (.SRA Files) to .fastq Files.

The command I used: "fastq-dump -I --split-files SRR1572697.sra" (one accession of them)

I got: "fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR1572697.sra

Written 0 spots total"

Strangely, 3 of them are converted to fastq files successfully, but for the other 3 sra files, I got the same informations just like above. So who knows how to solve this problem or convert these 3 sra files to fastq files?

Thanks a lot!

next-gen genome software error • 4.0k views
ADD COMMENTlink modified 4.0 years ago by george.ry1.1k • written 4.0 years ago by Cherry50
2
gravatar for george.ry
4.0 years ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

A 5 second Google suggests this is a version issue.  You are indeed using an old version of the sra toolkit (2.1.7 was released Oct2011).  Can you update the version you're using (downloads are here ... http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software ) and try this again before getting help with outdated software?

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by george.ry1.1k

Thank you so much, george.ry!

I didn't notice that the version is so old!!I have updated it and it works now!

ADD REPLYlink written 4.0 years ago by Cherry50

Glad to help!

ADD REPLYlink written 4.0 years ago by george.ry1.1k
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