[mira_talk] Re: Short notice: test version 2.9.44x2
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 18 Apr 2009 23:38:28 +0200
On Saturday 18 April 2009 Sucheta Tripathy wrote:
> I would be interested in testing this beta version. Only thing I would like
> to know is how much memory I will be needing for a genome of size approx.
> 100 MB. I have a limitation with the memory usage.
Hello Sucheta,
this actually is something I'd like to find out myself. If I remember
correctly, you had some 900k Sanger reads, right? Now, if MIRA uses more than
40 to 50 GiB, then I'd think that something happened I did not foresee.
For a "quick" first test, please start MIRA like this:
mira --project=... --job=genome,denovo,normal,sanger
-GE:not=4 -DP:ure=no -CL:pvlc=no -SK:mchr >&log_assembly.txt
(other switches at will)
This starts MIRA and turns off the most time consuming tasks so that you
comparatively quickly get an idea how things behave.
- if you want to use more threads during skim, increase -GE:not
- if you have less than 32 GiB memory, set -SK:mchr to 4092 (or less if really
tight)
I'm curious how it's going to run ...
Regards,
Bastien
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