I downloaded sra-toolkit from sra website for 64bit Windows.
After extracting I tested it from bin folder:
sra-toolkit\bin> fastq-dump --stdout -X 2 SRR390728
but it throws error:
2015-12-15T09:54:40 fastq-dump.2.5.5 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table
What may be the cause and how to get it working?
2 answers
Occasionally it needs this
vdb-config --restore-defaults
•
written
by
Istvan Albert
post on their github as an issue. As with many other bioinformatics software the sratookit produces incredibly user-unfriendly error messages even when the problems may be simple - I got this cryptic error myself, one of these typically fixes it,delete the cache directory, resinstall the whole thing etc.
•
written
by
Istvan Albert
Their issue tracker is here: https://github.com/ncbi/sra-tools/issues
•
written
by
Matt Shirley
This worked also for me to resolve another similar problem reported at A: Sra to fastq conversion err :
err: name not found while resolving tree within virtual file system module
Just download the fastq file from ENA. When possible, make your life simpler and avoid SRA files :)
the problem there is that ENA can be excruciatingly slow, sratoolkit is a genius idea in that it allows us to download just a subset of the data, which often is sufficient to verify a statement or check a result - alas it is not implemented the right way and the error messages are terrifyinly inefficient - what we really need is a tool to download fastq/bam files partially or download just 1% of the data.
•
written
by
Istvan Albert
On this side of the pond ENA is quite quick :)
But yes in an ideal world SRA would be the better route.
whoa! indeed. I never realized this, my a whole SRA world as I know it came crashing down. In my demos it is always so fast, but then of course because at some point in life I did indeed download these files ...
Log in to answer this question.
-
Error Code 3 with fastq-dump
written by hgrsce •
-
How to convert to .SRA files to .FQ (FASTQ)
written by Mariana •
-
sra-toolkit and fastq-dump error
written by chloisf •
-
fastq-dump error for restricted data from dbGAP
written by Rashedul Islam
-
fast-dump error, SRA Toolkit is Updated???
written by oars
-
SRA file download from NCBI
written by 1234anjalianjali1234 •
-
problem in fastq-dump of SRA file
written by majeedaasim •
-
download sra files with sra-toolkit: switch to HTTPS
written by marongiu.luigi
-
Is there a way to download FASTq files from SRR IDs?
written by Paul
-
Problem accessing SRA data using sratoolkit.
written by Naren
I can start the download from my current site. The file size is about 950 Mb. Thus the item is available from NCBI. The two major problem I have faced with SRA toolkit are: