Question: Prefetch command is not able to download sra file
0
gravatar for patanjal
2.6 years ago by
patanjal0
patanjal0 wrote:

While trying to download the sra file SRR2079558 using prefetch command, I am receiving this error message. I have already installed sra-toolkit. Could you please suggest something

"theranosis@DESKTOP-B2KQHTU:~$ prefetch SRR2079558
Maximum file size download limit is 20,971,520KB

**2018-04-13T13:14:41 prefetch.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR2079558' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )
Redirected!!!
2018-04-13T13:14:42 prefetch.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2018-04-13T13:14:42 prefetch.2.3.5 err: path not found while resolving tree within virtual file system module - 'SRR2079558' cannot be found.**
theranosis@DESKTOP-B2KQHTU:~$"
ADD COMMENTlink modified 2.6 years ago by Carambakaracho2.2k • written 2.6 years ago by patanjal0

When possible just get the fastq data directly from EBI-ENA. Like in this case SRR2079558.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by GenoMax93k

I could load it without problem. Try upgrading to the current version of the toolkit.

ADD REPLYlink written 2.6 years ago by ATpoint42k
0
gravatar for Carambakaracho
2.6 years ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:

As ATpoint mentioned: an upgrade will fix your problem. The error is clearly stated at the end of the lines:

[...] Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )

[...] Scheme is 'https'

Follow the provided link for more information

ADD COMMENTlink written 2.6 years ago by Carambakaracho2.2k
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