Problem while downloading RNAseq data from NCBI via command line

Question

[BCArg]

Dear all,

I am trying to download a few RNAseq data from NCBI using SRA toolkit with the following command:

fastq-dump --gzip SRR924395

and I'm getting the following error:

fastq-dump.2.6.3 err: function unsupported while opening file within network system module - log failure: RC(rcText,rcString,rcConverting,rcBuffer,rcInsufficient) in 'error with http open '$(U)''
2016-08-03T07:08:15 fastq-dump.2.6.3 err: item not found while constructing within virtual database module - the path 'SRR924395' cannot be opened as database or table

I have already used the SRA toolkit and the very same command to download this very same RNAseq data, but I was elsewhere (in an University, now I am using the wired connection from a company), so I am afraid I cannot download the data because of the settings of my new internet connection? In that case, does anyone know the correct internet settings?

What is the weirdest is the fact that I can download one specific RNAseq data (SRR924399) with the following command:

fastq-dump --gzip SRR924399

but for all the other data that I tried, I got the above mentioned error. I am running Linux 14.04, 64-bit. I am using SRA toolkit version 2.6.3

Thanks in advance.

Answer 1

[microfuge]

I have seen this issue when pulling sratoolkit from apt-get repo. Reinstalling sratoolkit by direct download from NCBI seemed to do the trick for me.

[BCArg]

I actually installed the older version (2.6.3) directly from the NCBI website. I un-installed that version and installed the newest one (2.7.0) yet I am getting the same error message.

Answer 2

[Devon Ryan]

It's best to check if ENA has the fastq files before bothering with fastq-dump. In this case, it has the sample in fastq format already.

[BCArg]

Thanks, that's indeed a good call. Unfortunately the data that I am interested in (SRR2136270, SRR2136269, SRR2136266 and SRR2136265) are not yet available on ENA (they were uploaded just on 01.Aug.2016).

[Devon Ryan]

You might have to download the SRA files then. Also, always use the most recent version of the SRA toolkit, half the time older releases don't work.

[BCArg]

oh really? Indeed I checker today that there is a newer version of the SRA toolkit. Would you have any advise on how to uninstall the old version of the toolkit (I am wondering whether I use purge or uninstall i.e. whether I remove all the dependencies)? Thanks again

[Devon Ryan]

It doesn't matter which method you use.

[BCArg]

I was advised from people from the NCBI not to do any of those, rather manually removing the directory with rm -rf. Although I am still getting the same error message with the newest version. I also noticed a very old version of the toolkit 2.1.7 installed on my /usr/bin directory, though I have no idea where that comes from

Answer 3

[igor]

I've had trouble with fastq-dump using an accession number as well. I find it more reliable to wget the SRA files and then run fastq-dump on that.