SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
velvet assembler, roadmaps bioinf Bioinformatics 12 02-06-2013 08:03 AM
RNAseq quantification - Velvet assembler seq4franken RNA Sequencing 9 11-17-2012 09:44 PM
meta-velvet returns nodes instead of contigs in assembly? deprekate Bioinformatics 2 10-25-2012 02:53 PM
Velvet assembler bioinf Bioinformatics 31 08-24-2011 10:19 AM
velvet assembler contigs into gbrowse Zimbobo Bioinformatics 0 04-15-2010 02:36 PM

Reply
 
Thread Tools
Old 10-20-2013, 01:04 PM   #1
rahularjun86
Member
 
Location: Frankfurt(M), Germany

Join Date: Jan 2011
Posts: 58
Default Does velvet assembler use RAM of all nodes altogether?

Dear All,

I have been doing an assembly using four lanes of Illumina Hiseq. I have 300bps, 800bps, 8kb and 20Kb insert libraries. Genome size is 80 MB and genome coverage of reads is more than 350x.

By calculating the RAM requirement for this assembly, it turned out that I need around 700GB of RAM for single assembly. I have been submitting velvet jobs on a cluster using PBS scripts, demanding for 32 nodes and 12 processors. Since, 24GB of RAM has been attached per node. If I calculate 32*24 it is equal to 768 GBs, which looks fine for the job submission. But, unfortunately all of my jobs are getting struck after generating velveth results.

My question is, in this kind of run will velvet use whole 768 GBs RAM on total nodes or will it use only 128 GBs ob a single node? I would really appreciate your response.

Thank you so much in advance!

Best regards, Rahul
__________________
Rahul Sharma,
Ph.D
Frankfurt am Main, Germany
rahularjun86 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 10:52 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO