error report：while running fastq-dump

Question

[zhenghanl1020]

Hi,I am trying to convert to SRR029687.sra to .fastq file.I am using the MS Windows 64 bit architecture executable. 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 '[e-mail]' for assistance.
=============================================================

Answer 1

[komal.rathi]

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.

[zhenghanl1020]

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 '[e-mail]' for assistance.
=============================================================

[komal.rathi]

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?

[rakeshmbb]

Hi komal.rathi..I am facing the same problem. How did u solve your problem. Please share

[li.anlin666]

me too , i also have the problem of that!

Answer 2

[seta]

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

[zhenghanl1020]

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

[seta]

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

[zhenghanl1020]

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

[seta]

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.

Answer 3

[zeguo.sun]

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

[zhenghanl1020]

Thanks!

Answer 4

[Ming Lu]

Try

sudo fastq-dump SRR029687

directly

[WouterDeCoster]

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.

[Ming Lu]

but it worked for me.

[hamarillo]

it's a terrible practice. almost makes me wish for a downvote button :(