[mira_talk] Re: 454 mapping

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 10 May 2012 23:09:38 +0200

On May 10, 2012, at 18:14 , davis gimode wrote:
> You are probably right. dmesg gives me this:
> [  274.865778] Out of memory: Kill process 2199 (mira) score 900 or
> sacrifice child
> [  274.865782] Killed process 2199 (mira) total-vm:5177844kB,
> anon-rss:2843432kB, file-rss:0kB
> 
> I guess I will have to try run the job on a high performance computing
> platform..

Ahhhmmm ... my laptop has 2 GiB and is 2 years old. High performance computing 
nowadays certainly starts at bit more higher than 3 GiB, I think :-)

BTW, I quickly looked at the numbers you posted. 60k contigs with 89 megabases 
as backbone will need quite some memory just for the contigs, my guess is 
around 8 to 10 GiB just for those. Then come your reads.

B.




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