Downloading SRA data by prefetch command
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
Entering edit mode
6.1 years ago

You have two choices

  1. Use

  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 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

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


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