Question: SRA toolkit internet settings
0
gravatar for BCArg
2.9 years ago by
BCArg60
UAntwerpen
BCArg60 wrote:

Dear all,

does anyone know if the SRA toolkit require specific internet settings (e.g. proxy servers, firewall, IPv4 or IPv6 etc) that must be met in order for its application that require download via HTTP to work correctly? I've recently described my issue in this topic and I now believe the problem is related to my current internet settings because:

  1. Those issues started when I started using my current internet connection - I've never experienced any problem while using the toolkit from my previous institution
  2. Yesterday, from home, I could use the command ./prefetch SRR924397 to download via HTTP. Today, at the office, I got the following error message while running the same command from the very same directory:

    2016-08-05T10:03:42 prefetch.2.7: 1) Downloading 'SRR924397'... 2016-08-05T10:03:42 prefetch.2.7: Downloading via http... 2016-08-05T10:03:42 prefetch.2.7 int: function unsupported while opening file within network system module - failed to open file for http://sra-download.ncbi.nlm.nih.gov/srapub/SRR924397 2016-08-05T10:03:42 prefetch.2.7 int: self NULL while reading file within file system module - http://sra-download.ncbi.nlm.nih.gov/srapub/SRR924397: Cannot KFileRead 2016-08-05T10:03:42 prefetch.2.7: 1) failed to download SRR924397

I am using the most up to date version of the toolkit (2.7.0) and running on Ubuntu 14.04 LTS 64-bit

Best regards.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by BCArg60
1

Howto use NCBI programs behind a HTTP proxy

ADD REPLYlink written 2.9 years ago by piet1.7k

Save yourself some heartache and get the fastq files from ENA directly. Click on the links. Subsequent page will have the fastq file links.

ADD REPLYlink written 2.9 years ago by genomax68k

The trouble is the reads I now want to download are not yet available on ENA.

ADD REPLYlink written 2.9 years ago by BCArg60
1

Then grab the .sra file here and then fastq-dump locally.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax68k

that's a good solution. Would you kindly send me the link where you could select to download the .sra file? The link you sent me was already the option to either download of open the file.

ADD REPLYlink written 2.9 years ago by BCArg60

Browse under ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ and then select based on Run/Experiments etc. Data is arranged in folders and you can drill down to the accession number you want.

ADD REPLYlink written 2.9 years ago by genomax68k

Brilliant, that solves my problem, thanks a million.

ADD REPLYlink written 2.9 years ago by BCArg60
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