Question: Does Velvet Assembler Use Ram Of All Nodes Altogether?
1
gravatar for Rahul Sharma
6.5 years ago by
Rahul Sharma600
Germany
Rahul Sharma600 wrote:

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

genome assembly velvet • 2.5k views
ADD COMMENTlink modified 6.5 years ago by Chris Fields2.1k • written 6.5 years ago by Rahul Sharma600
1
gravatar for Chris Fields
6.5 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

I don't believe Velvet is distributed (e.g. works across nodes). If you need something capable of doing this you should look into ABySS.

ADD COMMENTlink written 6.5 years ago by Chris Fields2.1k
1

Agreed. Velvet only runs in SMP mode (multiple threads on a single node). Allocating multiple nodes is a waste of resources as they will never be used.

ADD REPLYlink written 6.5 years ago by Torst950
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