Question: Problem accessing SRA data using sratoolkit.
0
gravatar for Nari
4.1 years ago by
Nari870
United States
Nari870 wrote:

I am trying to access the sra data via sratoolkit.but following error occurs after I enter the test command. 

F:\sratoolkit\bin>    fastq-dump.exe -X 5 -Z SRR390728

2015-10-09T08:39:43 fastq-dump.2.5.2 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

I also configured using these instructions.

Still unable to access.

 

latest • 4.3k views
ADD COMMENTlink modified 3.7 years ago by navankutty10 • written 4.1 years ago by Nari870

If you already have the SRR390728.sra file in your folder, then only it works. Use prefetch to download the data from the archive. Try to use a Linux system which will be more comfortable than windows.

ADD REPLYlink modified 2 days ago by RamRS24k • written 4.1 years ago by venu6.3k

Hi! even I got the same error.. I also tried this..

vdb-config --restore-defaults                                                                                
Unknown argument restore-defaults
2016-03-16T10:02:38 vdb-config.2.1.7 err: param unknown while parsing argument list within application support module - While calling ArgsMakeAndHandle

How to solve this ??

Thanks in advance..

ADD REPLYlink modified 2 days ago by RamRS24k • written 3.7 years ago by navankutty10

You may want to search with the SRA # at EBI ENA: http://www.ebi.ac.uk/ena. You can find links for fastq sequence files once you open the record page. No need to struggle with sratoolkit.

ADD REPLYlink written 3.7 years ago by genomax74k
1
gravatar for Istvan Albert
4.1 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

Try

vdb-config --restore-defaults

I am collecting errors on tools on the handbook webpage:

https://www.biostarhandbook.com/unit/setup/how-to-install-everything.html#sratoolkit

ADD COMMENTlink modified 2 days ago by RamRS24k • written 4.1 years ago by Istvan Albert ♦♦ 81k
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