[mira_talk] Re: Skim hits error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 28 Sep 2010 21:57:41 +0200
On Donnerstag 23 September 2010 Shabhonam Caim (TGAC) wrote:
> Assembly with 1 Lane of Illumina ~32 million reads
> About 1.5 million 454 reads
Hello Shab,
I fear that this will be one of the projects where MIRA has to capitulate. You
are operating at the border of what MIRA can theoretically handle ... and
crossed it.
> Expected genome size ~150 Mb
> Having to write log files to NFS drive
That is ... bad.
> I did try the miramem and I got the memory estimate around 80Gb, but its
> utilising over 200Gb of memory.
Can you please send me the whole log file? I'd like to know where the memory
goes.
> Here is the latest error message from MIRA.
> [...]
> "More than 2^31 skim hits would be taken ... this was not foreseen yet.
> Please contact the author."
That's the boundary the project crosses. I'm working on something to alleviate
this problem, but it will take some time before I can roll that out, I first
have a bug fix version on my list.
Best,
Bastien
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