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Old 05-07-2012, 03:04 AM   #1
vinila86
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Default problem while using sra tool kit

hi, I need to convert my SRA file into fastq format.. for that i download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces...?view=software. I am using fedora 64 bit linux operating system and choose CentOS Linux 64 bit architecture as sra toolkit compressed file.

I Decompress the downloaded file, and copy the fastq-dump file to system path. Then I Convert SRA to fastq by using the command
fastq-dump <SRA archive file>

but I am getting an error like this..

2012-05-06T19:18:21 fastq-dump.2.1.12 err: column not found while opening table within short read archive module - failed SRR069603.sra
Written 0 spots total

=============================================================
An error occurred during processing.
A report was generated into the file '/root/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to '[email protected]' for assistance.
==========================================================

somebody please tell me why it is happening and the solution..it is urgent!!

thank u!!
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Old 05-07-2012, 04:11 AM   #2
Bukowski
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Default

Apparently you're not the only person with this issue:

http://seqanswers.com/forums/showthread.php?t=17508

Have you actually done what is suggested and sending the error report to NCBI? What is in the error report anyway? It might hold a clue..
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Old 05-07-2012, 05:07 AM   #3
vinila86
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thank u for the replay,
well, I am copying the error report which i got...

<Report>
<Run>
<Cwd>/root/Desktop/sratoolkit.2.1.10-centos_linux64</Cwd>
<CommandLine argc="2">
<Arg index="0" value="./bin/fastq-dump"/>
<Arg index="1" value="SRR069603.sra"/>
</CommandLine>
<Result rc="RC(rcSRA,rcTable,rcOpening,rcColumn,rcNotFound)"/>
</Run>
<Configuration>
<Files count="2">
<File name="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/ncbi/config.kf
g"/>
<File name="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/ncbi/vdb-copy.
kfg"/>
</Files>
<refseq state="not found"/>
<krypto file="not found">/root/.ncbi/.vdbpass</krypto>
<sra state="not found"/>
</Configuration>
<Object path="/root/Desktop/sratoolkit.2.1.10-centos_linux64/SRR069603.sra" type="table" fs_type="archive" size="138873160">
</Object>
<SOFTWARE>
<VDBLibrary vers="2.2.6"/>
<Build static="true"/>
<Tool date="Mar 28 2012" name="./bin/fastq-dump" vers="2.1.12">
<Binary path="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/fastq-dump" type="alias" md5="f65c872ed7b695b92e646b3151133675">
<Alias resolved="fastq-dump.2">
<Alias resolved="fastq-dump.2.1.12"/>
</Alias>
</Binary>
</Tool>
</SOFTWARE>
</Report>

...............................is it because i am using fedora instead of CentOS??? please continue replay........ thank u
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Old 05-07-2012, 09:16 PM   #4
srasdk
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According to
ftp://ftp-trace.ncbi.nlm.nih.gov/sra...R069/SRR069603

The file size is 651,975,610

Fastq-dump reports size="138873160"

Either you ran out of disk space or file transfer was aborted. Try to download again.

You can use sra-dbcc command from SRA Toolkit to check if downloaded file is OK.
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Old 10-08-2012, 09:10 PM   #5
zeam
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Default How did you handle this problem?

Quote:
Originally Posted by vinila86 View Post
hi, I need to convert my SRA file into fastq format.. for that i download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces...?view=software. I am using fedora 64 bit linux operating system and choose CentOS Linux 64 bit architecture as sra toolkit compressed file.

I Decompress the downloaded file, and copy the fastq-dump file to system path. Then I Convert SRA to fastq by using the command
fastq-dump <SRA archive file>

but I am getting an error like this..

2012-05-06T19:18:21 fastq-dump.2.1.12 err: column not found while opening table within short read archive module - failed SRR069603.sra
Written 0 spots total

=============================================================
An error occurred during processing.
A report was generated into the file '/root/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to '[email protected]' for assistance.
==========================================================

somebody please tell me why it is happening and the solution..it is urgent!!

thank u!!
Hi vinila86,

Recently I have enconter the same problem. I want to know how did you handle this problem finally.

I have used sra-dbcc to check the file, and the report was as follows:
================================
2012-10-09T04:05:06 sra-dbcc.2.1.6 info: Table 'SRR488770.sra' ok
================================
Thanks.

Last edited by zeam; 10-08-2012 at 09:12 PM. Reason: add some information.
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Old 10-17-2012, 09:15 AM   #6
jfgout
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Cool

I had the same problem. Simply updating the fastq-dump from 2.1.6 to the latest version (2.1.18) solved it.
Hope this helps.

Jeff
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Old 12-07-2012, 02:59 AM   #7
olesk
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Dear all,
I have been through all your frustrations:
- clicking like hell in the SRA archive and running in circles.
- downloading SRA tools (yes I know my platform!!!) and finding instructions in discrepancy with the outcome
- trying again - and again - reading the download guide - try again and again and again and after a while thinking that this would have corrected - and then again.
You do not wish to discuss memory problems, versions, columns, tables etc.
I have found two backdoors:
One is when you have found your SRR numbers:
Then you can download each file individually from your web-browser replacing the digits after SSR in this link:
http://www.ncbi.nlm.nih.gov/Traces/s...5&format=fastq
or multible seuences with a link like:
http://www.ncbi.nlm.nih.gov/Traces/s...5&format=fastq
The other is more clicking around:
- Find your study, your link may look like:
http://trace.ncbi.nlm.nih.gov/Traces...tudy=SRP013698
- In the experiment to your Right find the clickable “Show RUNs for each experiment” and click.
- Click one of the SRR numbers
- DO NOT click download – but click reads instead.
- Find the “Filtered download” and click.
- Now select which or all SRR’s you want and select FASTQ – or FASTA if preferred – and download in FASTx.gz starts
This reply is also meant as thanks to all the great people that brings these data to us and a friendly reminder that all these data could be made much more accessible to common users. Much of the problem is caused ordinary design flaws.
- best
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Old 04-14-2013, 11:51 AM   #8
Arouth
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Hi,
I had a similar problem. You may have to specify the accession directly using the '-A' option. Without this, the accession is taken directly from <path>.

For example, if this fails:
/files/fastq-dump SRR234234.sra

Then try:
/files/fastq-dump -A SRR234234 SRR234234.sra

Hope this helps.
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Old 08-28-2013, 12:39 AM   #9
aleferna
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Default still same problem with column not found...

I have the same problem with fastq-dump.2.3.2,
column not found while opening table within short read archive module
tried -A, the perl configuration, the jar, nothing seems to work??


I'm doing fastq-dump SRR000712.sra from bash as I've always done?
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Old 08-28-2013, 05:16 AM   #10
GenoMax
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As strange as this may sound have you tried to provide the full file path to the sra file when doing the fastq-dump? Several people have reported that to work for various fastq-dump related issues.

/files/fastq-dump /full_path_to/SRR000712.sra

Update: I just tried the file myself. Getting the same error.

Last edited by GenoMax; 08-28-2013 at 05:56 AM.
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Old 08-28-2013, 06:50 AM   #11
aleferna
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Yeap tried wiht the full path, when I do this the error message changes from file not found to the problem with the columns?
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Old 08-28-2013, 07:02 AM   #12
GenoMax
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Oddly sra-dump seems to work. Try it.

These data are from 2008 so who knows what has changed with SRAtoolkit since that time.
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Old 08-28-2013, 08:31 AM   #13
dpryan
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Sometimes, it's easier to just grab the gzipped fastq file(s) from ENA
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Old 04-02-2014, 05:06 PM   #14
eckofoid
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Although grabbing the gzipped file always works, it also can take hours, as opposed to a few minutes with Aspera.

On a separate note, I can't find any useful information about how to use sra-dump. Could somebody give a couple of examples please?
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