Downloading SRA data by prefetch command
1
1
Entering edit mode
6.1 years ago
hasani.iut6 ▴ 70

I want to download a SRA data (SRA052842) with the prefetch command in command line of Ubuntu, The prefetch command is belonged to SAM tools package, so I've used the following command:

prefetch SRA052842

and I've faced with following error:

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

2015-11-07T06:28:05 prefetch.2.3.5 err: path not found while resolving tree within virtual file system module - 'SRA052842' cannot be found.

Where is the problem? How can I fixed it?

prefetch SRA • 8.4k views
ADD COMMENT
3
Entering edit mode
6.1 years ago

You have two choices

  1. Use http://www.sradownload.com

  2. Use a FTP client program such as Filezilla under an anonymous identity

    • Just download and install the program
    • Create a new connection pointing at ftp-trace.ncbi.nhi.com as the server
    • Hit the advanced tab
    • Fill the remote directory with /sra/sra-instant/reads

And you will be allowed to choose your SRA data by Exp, Run, Sample and Study

ADD COMMENT
0
Entering edit mode

I am downloading just now some SRA data. In using Filezilla, without limits in the downloding speed and using the latest version of this program, I wasn't able to download at a higher speed of 1,4Mb/s

With wget I could download the data at 10Mb/s.. just using the same URL that Filezilla can provide

This means that instead downloading my data for over 6h, I could do it in only 1h

ADD REPLY

Login before adding your answer.

Traffic: 2703 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6