SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error when using SRA toolkit on server KatherineDuch Illumina/Solexa 0 02-07-2017 07:39 PM
new usage of SRA toolkit/ SRA archive data download Retro Bioinformatics 7 08-20-2015 03:05 PM
SRA -> FastQ, Problem with SRA toolkit? kelseyca Bioinformatics 12 05-23-2013 12:59 PM
SRA Toolkit in ubuntu 12.04 shrujan Bioinformatics 33 04-18-2013 04:11 PM

Reply
 
Thread Tools
Old 06-18-2017, 01:46 PM   #1
cbmckni
Junior Member
 
Location: Clemson, SC

Join Date: Jun 2017
Posts: 2
Default IBM Power8: Need help accessing NCBI genomes WITHOUT SRA toolkit.

Hello everyone,

I joined because I need help setting up a research environment on an IBM Power8 server. The tools I will be using to analyse genomes are all included in Biobuilds(which I installed without any issues), except for one. We will be using genomes stored in NCBI's repository, which requires you to install NGS/SRA toolkit to download them.

Here is an example of a command I would need to run:

$ fastq-dump -X 5 -Z SRR390728

My issue is this: NGS/SRA toolkit does not offer support for the power8 architecture. I have tried normal installation and installing from source code, both of which gave me error messages along the lines of "unsupported architecture"(which is Ubuntu ppc64le).

Does anyone know a way to download .sra files and convert them to fastq, without using the toolkit?

I have tried a wget command I found online, but that gave me a message along the lines of "please download SRA toolkit".

Workaround:

If I am unable to figure this out soon, I will be forced to download and convert the data using Clemson's Palmetto Cluster, then upload the files to github, then download them to the IBM server(which is a huge waste of time and resources).

Any advice, or simply a point in the right direction would be greatly appreciated.

Thanks,

Cole
cbmckni is offline   Reply With Quote
Old 06-18-2017, 03:44 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,574
Default

You can download fastq files directly from EBI-ENA. No need for SRAtoolkit. Example using your SRR# here.
GenoMax is offline   Reply With Quote
Old 06-18-2017, 05:38 PM   #3
cbmckni
Junior Member
 
Location: Clemson, SC

Join Date: Jun 2017
Posts: 2
Default Thanks!!! @Genomax

This kind of pointer is exactly what I was looking for. Thank you so much for your abrupt response.

Do you have any tips on bulk downloading entire data sets from the command line?

Here is one of such sets:

http://www.ebi.ac.uk/ena/data/view/PRJEB6754

Writing my own script is the first thing that comes to mind, but I am sure there is another way....
cbmckni is offline   Reply With Quote
Old 06-19-2017, 12:58 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,574
Default

Take a look at ENA API. I am not sure if it works with EBI SRA data but worth a try.
GenoMax is offline   Reply With Quote
Old 07-01-2017, 08:38 AM   #5
cochrane
Junior Member
 
Location: UK

Join Date: Jan 2009
Posts: 4
Default

Quote:
Originally Posted by GenoMax View Post
Take a look at ENA API. I am not sure if it works with EBI SRA data but worth a try.
Have a look at enaGroupGet at https://github.com/enasequence/enaBrowserTools - command line downloads including fastq from ENA.
cochrane is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:16 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO