Question: sra toolkit program fastq-dump question.
1
gravatar for jinhwa1112
4.2 years ago by
jinhwa111210
Korea, Republic Of
jinhwa111210 wrote:

hello.

I encountered an error during the execution of the fastq-dump using the SRA data. 

(SRA data : SRR1597832, SRR1597841 etc...)

first error message is as follows:

2015-01-27T09:40:46 fastq-dump.2.4.3 err: binary large object corrupt while read
ing binary large object within virtual database module - failed

i'm use command :

fastq-dump --split-3 SRR1597832.sra

In order to solve this problem.....................

 

1. SRR1597832 data Re-download

URL : ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR159/SRR1597832/

The error message is as follows:
 

G:\sratoolkit.2.4.3-win64\bin>fastq-dump --split-files SRR1597832.sra
2015-01-29T09:15:39 fastq-dump.2.4.3 err: binary large object corrupt while read
ing binary large object within virtual database module - failed SRR1597832.sra

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

2. command change

The error message is as follows:
 

G:\sratoolkit.2.4.3-win64\bin>fastq-dump --split-files SRR1597832
2015-01-29T08:27:41 fastq-dump.2.4.3 err: buffer insufficient while executing fu
nction within transform module - failed SRR1597832

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

It is not possible to solve the problem.
Please help me.....
Please answer fast.
Thank you. 

error fastq-dump toolkit sra • 6.6k views
ADD COMMENTlink modified 4.1 years ago by DCGenomics310 • written 4.2 years ago by jinhwa111210

Please paste the contents of the ncbi_error_report.xml file so we can help you. 

ADD REPLYlink written 4.2 years ago by RamRS20k

Thank you for answers.

ncbi_error_report.xml file :

Moved to GitHub-Gist here: https://gist.github.com/RamRS/b6bc032767fec796428f#file-biostars-128831-ncbi_error_report-xml

ADD REPLYlink modified 4.2 years ago by RamRS20k • written 4.2 years ago by jinhwa111210

I'm not sure what the problem is. While you're waiting for answers here, you should also email the XML file to sra@ncbi.nlm.nih.gov.

ADD REPLYlink written 4.2 years ago by RamRS20k

Already sent an e-mail.

Answer mail information.................

You downloaded an incomplete SRR1597832.sra file. You can use prefetch to

download SRR1597832.sra or use the command:
/g/sratoolkit.2.4.3-win64/bin/fastq-dump --split-files SRR1597832

This command does not need you to download the SRR1597832.sra first.  
 

Still not resolved.

 

ADD REPLYlink written 4.2 years ago by jinhwa111210

What is your machine configuration in terms of RAM?

ADD REPLYlink written 4.2 years ago by RamRS20k

My computer operating system Window 7 64bit.

Computer RAM 32.0GB.

ADD REPLYlink written 4.2 years ago by jinhwa111210

Hmmm, let's try this possible solution: Open  G:\sratoolkit.2.4.3-win64\bin and right click on fastq-dump, choose Properties. See if you have an Unblock option (like the one shown here https://codingoutloud.files.wordpress.com/2010/02/dreaded-unblock.png ). If you see it, unblock and hit OK. Try the command again and check if the error persists.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by RamRS20k

Hmmm.....Check the results are not visible...

instead, set the compatibility mode. win7.

Currently running again.

 

 

ADD REPLYlink written 4.2 years ago by jinhwa111210
1
gravatar for DCGenomics
4.2 years ago by
DCGenomics310
United States
DCGenomics310 wrote:

My understanding is that there is a networking error, and the situation is expected to be remedied by Monday.

ADD COMMENTlink written 4.2 years ago by DCGenomics310

download it again.

ADD REPLYlink written 4.1 years ago by jinhwa111210
1
gravatar for george.ry
4.2 years ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

If it's not playing ball, just get the fastq files directly:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR159/002/SRR1597832/

That's generally easier than getting the sra files and then using the slow dump command anyway :p

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by george.ry1.1k

NCBI SRR1597832 data fastq-dump program result data and the result is the same data?

ADD REPLYlink written 4.1 years ago by jinhwa111210
1
gravatar for DCGenomics
4.1 years ago by
DCGenomics310
United States
DCGenomics310 wrote:

A new version (2.4.4) of the sra toolkit has been released!

http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software

ADD COMMENTlink written 4.1 years ago by DCGenomics310

Thank you!

download new release..

ADD REPLYlink written 4.1 years ago by jinhwa111210
0
gravatar for Matt Shirley
4.2 years ago by
Matt Shirley8.9k
Cambridge, MA
Matt Shirley8.9k wrote:

The NCBI SRA is definitely acting strangely. Earlier today I was having similar issues. If you absolutely need the data right now you should be able to download the entire .sra file from the NCBI FTP site. It seems that the SRA Toolkit API for fetching archives is not working properly today...

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Matt Shirley8.9k

download it again.

ADD REPLYlink written 4.1 years ago by jinhwa111210
1

Are you asking people to download it again or are you saying you downloaded it again?

ADD REPLYlink written 4.1 years ago by RamRS20k

sorry.

I'm downloading the data again

ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR159/SRR1597832/

ADD REPLYlink written 4.1 years ago by jinhwa111210
0
gravatar for Tulip Nandu
4.1 years ago by
Tulip Nandu80
United States
Tulip Nandu80 wrote:

The reason you are getting the error is the deposited SRA file is in bam format and you would have to add the genome file to it.

Please take a look at

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=std

One option is to download the fastq file and directly follow the pipeline. On some exome sequencing data fastq dump doesnt work as efficiently or gives errors as the deposited data is in bam format and requires genome file. So from the below website we can directly download the fastq files for all sequencing experiments in GEO.

ADD COMMENTlink written 4.1 years ago by Tulip Nandu80

I guess OP's problem was solved when OP tried re-downloading the files.

ADD REPLYlink written 4.1 years ago by RamRS20k

Thank you.

I was already using the method proposed by you.(vdb-config (www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=std)

However, continuing an error occurs.

Thanks for the URL.

thank you.

 

ADD REPLYlink written 4.1 years ago by jinhwa111210

add file : prj_phs710EA_test.ngc

 

ADD REPLYlink written 4.1 years ago by jinhwa111210
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