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error report：while running fastq-dump

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 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================
sra-fastq sratoolkit
• 12,417 views • link
updated by hamarillo • hamarillo • written by zhenghanl1020 • zhenghanl1020

4 answers

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.

• 0 views • link
updated by Ram Ram • written by komal.rathi komal.rathi

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.
=============================================================
• 0 views • link
updated by Ram Ram • written by zhenghanl1020 • zhenghanl1020

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?

• 0 views • link
updated by Ram Ram • written by komal.rathi komal.rathi
Hi komal.rathi..I am facing the same problem. How did u solve your problem. Please share
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written by rakeshmbb • rakeshmbb

me too , i also have the problem of that!

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written by li.anlin666 • li.anlin666

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

• 0 views • link
written by seta seta

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

• 0 views • link
written by zhenghanl1020 • zhenghanl1020

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

• 0 views • link
updated by Ram Ram • written by seta seta

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

• 0 views • link
updated by Ram Ram • written by zhenghanl1020 • zhenghanl1020

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.

• 0 views • link
updated by Ram Ram • written by seta seta

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

• 0 views • link
updated by Ram Ram • written by zeguo.sun • zeguo.sun

Try

sudo fastq-dump SRR029687

directly

• 0 views • link
updated by Ram Ram • written by Ming Lu • Ming Lu

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.

• 0 views • link
written by WouterDeCoster WouterDeCoster

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

• 0 views • link
written by hamarillo • hamarillo

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