[mira_talk] Re: assembly parameters and more

Dear all, Bastien,

let me first thanks dr. Paces and dr. Duarte for the useful inputs


but we were afraid of having
issues with contaminating DNA and chimeras formed by whole genome
amplification, both of which in fact we have.


Ouch. Difficult organism to get growing?

yes, no culture available
*This* is most unusual. MIRA is a memory hog, but should not be that greedy. Can you please send me the output log, I'd like to check a few things.
I'm sorry but I'm not sure what file you mean. Is it the EdIt.log? that file is empty. or is it a file in the log folder? I'm pretty sure you already explained this in an older message but I really cannot find it, sorry. 



Then, while I look through that, restart your project with this:
mira -project=050309 -job=denovo,accurate,454,sanger,genome -GE:not=2 -AS:klrs=1 -AL:mrs=90 -CO:rodirs=15 
         454_SETTINGS -AS:mrl=80 -AL:mrs=90 -CO:rodirs=20:mrpg=10

There are a few other differences to your call:
- -SK:mnr is off as you should not need it for a simple bacterium. If yes, then
  you are in deep trouble anyway.
- -AL:mrs is higher to catch chimeras a bit earlier
- -CO:rodirs is set a bit stricter. This could lead to a few reads with
  sequencing errors not to be built in, but ... you have more than enough of
  them.
- -CO:mrpg has been increased for 454 reads. This is due to the high coverage
  you have which in turn might lead to sequencing errors, which might amass at
  a given position, to be wrongly seen as repeat. Given a coverage of 100, you
  could also try 20 or 30 for this value.
Ok, I tried exactly as you write but it stops because of 0.3% megahubs, so I guess I'm in deep trouble? I'm currently trying with mnr on, but I was not sure about this, maybe I should have set the allowed hubs to 0.4%? 
Now it's in the preassembly step and it is already swapping 1Gig

Thank you so much
Davide

--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria Facoltà di Veterinaria 
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095

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