Question: error report:while running fastq-dump
0
gravatar for zhenghanl1020
3.2 years ago by
China
zhenghanl10200 wrote:

Hi,I am trying to convert to SRR029687.sra to .fastq file.I am using MS Windows 64 bit architecture. The command I am running is fastq-dump -A D:\SRRdata\SRR029687.sra.

But after a while of running,it gives an error :

2014-10-27T01:55:32 fastq-dump.2.4.2 err: data insufficient while constructing header within virtual database module - failed /D/SRRdata/SRR029687.sra

=============================================================
An error occurred during processing.
A report was generated into the file 'C:\Users\acer/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

sra-fastq sratoolkit • 3.9k views
ADD COMMENTlink modified 11 weeks ago by Ming Lu0 • written 3.2 years ago by zhenghanl10200
4
gravatar for komal.rathi
3.2 years ago by
komal.rathi3.0k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.0k wrote:

I downloaded the file from here and run the following commands and it worked for me.

fastq-dump --split-3 ./SRR029687.sra
Rejected 217386 READS because of filtering out non-biological READS
Read 217386 spots for SRR029687.sra
Written 217386 spots for SRR029687.sra

​
fastq-dump -A SRR029687 ./SRR029687.sra
Read 217386 spots for SRR029687.sra
Written 217386 spots for SRR029687.sra

The file is pretty small (~134M). There shouldn't be any memory problem.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by komal.rathi3.0k

I tried your command, it can't be worked.

Here are the results.

D:\sratoolkit.2.4.2-1-win64\bin>fastq-dump D:\SRRdata\SRR029692.sra
2014-10-28T11:48:03 fastq-dump.2.4.2 err: data insufficient while constructing header within virtual database module - failed /D/SRRdata/SRR029692.sra

=============================================================
An error occurred during processing.
A report was generated into the file 'C:\Users\acer/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

ADD REPLYlink written 3.2 years ago by zhenghanl10200

zhenghanl1020 I have edited my answer. Also can you try using these commands on a different .sra file to check if there is anything wrong with the file? 

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by komal.rathi3.0k
Hi komal.rathi..I am facing the same problem. How did u solve your problem. Please share
ADD REPLYlink written 24 months ago by rakeshmbb0

me too , i also have the problem of that!

ADD REPLYlink written 8 weeks ago by li.anlin6660
1
gravatar for seta
3.2 years ago by
seta930
Sweden
seta930 wrote:

Hi,

I did not work with windows, but you can easily convert your file after installing sra-toolkit in Ubuntu and using this command in terminal:

fastq-dump SRR029687.sra

ADD COMMENTlink written 3.2 years ago by seta930

I don't have enough free space(100's of GB) on my PC installed with Ubuntu, so it can't be installed.

ADD REPLYlink written 3.2 years ago by zhenghanl10200

wow! you don't require 100 Gb free space, just 10-20 Gb is enough. 

ADD REPLYlink written 3.2 years ago by seta930

Please teach me how to installe this tool. I have tried it for many times but failed!

2014-10-28 20:13 GMT+08:00 setareh227 on Biostar

ADD REPLYlink written 3.2 years ago by zhenghanl10200

linux is an operating system not tool, I can't help you to install it here. you can get help from people who work in the computer field in your university. However, I suggest you to install Ubuntu 13.1.

ADD REPLYlink written 3.2 years ago by seta930
0
gravatar for zeguo.sun
3.2 years ago by
zeguo.sun0
China
zeguo.sun0 wrote:

Hi,

   I've just faced with the same problem a few days ago and I wrote a letter to sratoolkit. They ask me to run the prefetch commend under the bin folder to get the needed reference. Like prefetch ERR053953.sra. It seems to work.I guess it may get you some help.

Good luck

ADD COMMENTlink written 3.2 years ago by zeguo.sun0

Thanks !

2014-11-10 9:54 GMT+08:00 zeguo.sun on Biostar <notifications@biostars.org>:

ADD REPLYlink written 3.2 years ago by zhenghanl10200
0
gravatar for Ming Lu
11 weeks ago by
Ming Lu0
Australia
Ming Lu0 wrote:

Try

         sudo fastq-dump SRR029687

directly

ADD COMMENTlink written 11 weeks ago by Ming Lu0

I don't think this is a good enough reason to use sudo and it would seriously surprise me if it would make a difference. You shouldn't use sudo for just running software, only for 'system administrator purposes' such as installing software.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by WouterDeCoster25k

but it worked for me.

ADD REPLYlink written 5 weeks ago by Ming Lu0
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