Question: sra-toolkit not working
1
gravatar for Nari
3.3 years ago by
Nari870
United States
Nari870 wrote:

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.

sra-toolkit fastq • 3.1k views
ADD COMMENTlink modified 3.3 years ago by Istvan Albert ♦♦ 79k • written 3.3 years ago by Nari870

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:

1) if you need a proxy to access the internet, you have to configure this explicitely for SRA toolkit

2) make sure, that you have enough disk space in the cache directory used by SRA toolkit. By default, the cache directory is placed in your HOME directory. If your HOME is mounted via NFS or is otherwise restricted in size, the default is a very bad choice.  

 

ADD REPLYlink written 3.3 years ago by piet1.6k
5
gravatar for Istvan Albert
3.3 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

Occasionally it needs this

vdb-config --restore-defaults

ADD COMMENTlink written 3.3 years ago by Istvan Albert ♦♦ 79k

The solution works for others but in my case no effect.

ADD REPLYlink written 3.3 years ago by Nari870
1

Their issue tracker is here: https://github.com/ncbi/sra-tools/issues

ADD REPLYlink written 3.3 years ago by Matt Shirley8.9k

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.  

ADD REPLYlink written 3.3 years ago by Istvan Albert ♦♦ 79k

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
ADD REPLYlink written 2.8 years ago by Arnaud Ceol840
3
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

Just download the fastq file from ENA. When possible, make your life simpler and avoid SRA files :)

ADD COMMENTlink written 3.3 years ago by Devon Ryan88k
2

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. 

ADD REPLYlink written 3.3 years ago by Istvan Albert ♦♦ 79k
1

SRA toolkit always downloads the whole SRA file to your local disk and stores it in a hidden directory. After download has completed, you may extract only part of the data from your local copy. 

ADD REPLYlink written 3.3 years ago by piet1.6k

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 ...

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Istvan Albert ♦♦ 79k

On this side of the pond ENA is quite quick :)

But yes in an ideal world SRA would be the better route.

ADD REPLYlink written 3.3 years ago by Devon Ryan88k
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