[mira_talk] Re: Short notice: test version 2.9.44x2

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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