Question: download sra files with sra-toolkit: switch to HTTPS
0
gravatar for marongiu.luigi
18 months ago by
Germany, Mannheim, UMM
marongiu.luigi380 wrote:

Dear all,

I want to use SRA-tools to download sra files. I installed the package with

sudo apt install sra-toolkit

and the installation must have been successful because if I type for instance prefetch -V I get prefetch : 2.3.5 and fastq-dump -V gives fastq-dump : 2.3.5.

I tried to download the files SRR390728 and SRR390728 provided in the manual pages of the sra-tools from NCBI. But if I do, as indicated, I get:

~$ fastq-dump -X 5 -Z SRR390728 
2017-10-04T22:08:26 fastq-dump.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR390728' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )

    Redirected!!!

    2017-10-04T22:08:28 fastq-dump.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https' 2017-10-04T22:08:28 fastq-dump.2.3.5 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

and

~$ prefetch SRR390728

Maximum file size download limit is 20,971,520KB

2017-10-04T22:09:29 prefetch.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR390728' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )

Redirected!!!

2017-10-04T22:09:31 prefetch.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2017-10-04T22:09:31 prefetch.2.3.5 err: path not found while resolving tree within virtual file system module - 'SRR390728' cannot be found.

the indicated page says:

ATTENTION:

sra-tools has transitioned to all HTTPS access as of October 7, 2016 with release 2.8.0. It is critically important that you update all of your binaries and your configuration files.

This is in response to OMB memorandum M-15-13 issued on June 8, 2015, requiring all Federal HTTP servers to stop using (simple) HTTP and switch to HTTPS.

Please update your software as soon possible to give some time to ensure continued operation.

Proxy users take note - this complicates proxy usage somewhat. We will create a Wiki page dedicated to supported proxy configuration and firewall settings to help users during the conversion.

How can I make this switch to HTTPS?

rna-seq next-gen • 2.1k views
ADD COMMENTlink written 18 months ago by marongiu.luigi380

You appear to have downloaded (or have an older version sticking around in your $PATH). You could try to see if you have more than one version installed (by doing a find / -name fastq-dump. If you have two versions then there should be two entries with that name. Check them individually with -V option with full path and then use the one that is the latest.

Better still search ENA with any accession numbers you are interested in and download the fastq files directly.

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax65k

I doubt I have multiple installations since I installed it only once. anyway in the official download page there is version 2.8.2-1. I'll try to use that instead. Tx

ADD REPLYlink written 18 months ago by marongiu.luigi380

I removed the installation using sudo apt-get remove --auto-remove sra-toolkit and sudo apt-get purge --auto-remove sra-toolkit then i downloaded the new version and extracted in /ucr/local/lib/ after renaming it sratools and modified the .bashrc fila adding export PATH="/usr/local/lib/sratools/bin:$PATH". Then when I typed prefetch -V I got prefetch : 2.8.2. Now it is working fine, so it was just an issue of version package. Thanks again.

ADD REPLYlink written 18 months ago by marongiu.luigi380

The files you are loading are both mirrored at the ENA, directly accessible as fastq. You can also download via aspera.

ADD REPLYlink written 18 months ago by ATpoint15k
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