[mira_talk] Re: Out of memory when lots of memory available...

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 1 Jul 2010 20:18:07 +0200

On Donnerstag 01 Juli 2010 Lionel Guy wrote:
> I'm using mira 3.1.15 to assemble de novo a small (1.6 Mb) bacterial
> genome, with an acceptable level of repeats (had 1-2 megahubs). I'm
> using paired-end and non-paired-end 454 reads (300 kreads) and some long
> Sanger reads (separate fosmid assemblies, 5-20kb long).
> 
> I've already been running a very similar assembly (but with less Sanger
> reads) earlier with a previous version of mira (3.0.4, if I remember
> correctly), and had no particular problems.
> 
> Now I'm running it again and got three times out of memory troubles, at
> different points of the assembly, and running it on different machines
> (twice on a local machine with 8Gb, and once on a cluster node with 24
> Gb).

Ehm ... out of memory with 300k reads? This should not really happen. Could I 
have a look at that complete data set?

B.

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