Problem accessing SRA data using sratoolkit.

Question

[Naren]

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.

[venu]

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.

[navankutty]

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..

[GenoMax]

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.

Answer 1

[Istvan Albert]

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