[mira_talk] Re: assembly parameters and more

Hi Bastien, all,
Thanks for the answer!
I'm currently running 2.9.43 at 'normal' level with mask on. I started 2.9.43 before you told me to, must be telephatic ;)
The first pass went smoothly (around 33hours) but now in the second pass it started swapping (now 6 gigs), I'll keep you informed.
Maybe I should assemble just the half titanium plate and use the half normal gs-flx afterwards to close the gaps? 

thanks
D.





On Sunday 15 March 2009 Davide Sassera wrote:

I hope I understood correctly what you need and that the file I'm
sending is the right one.


Hi Davide,
thanks for the files you sent. Took me some time to have a look at, but they were basically what I needed.
Looks like there is a combination of a few things going on. I made a some tests and discovered that massive coverage together highly repetitive data and turning on masking nasty sequences gave the behaviour you saw. 

First: the coverage (and megahubs)
100x is already quite massive for de-novo. If the genome you have contains some nasty surprises (say, a repetitive element, longer than a read, is contained 15x in the genome), then this explains the 1500x coverages you saw in some passes of MIRA. In earlier times one saw this kind of coverage only for EST sequencing projects ... in non-normalised libraries.
Therefore, these things tend to trigger the megahub detector ... and I cannot really blame it for that :-) 


Second: the long runtime and insane memory requirements
These were triggered by the massive coverage in conjunction with the masking of nasty repeats ... and a "security feature" I built into MIRA that backfired. Short story: So as not to loose alignments when parts of it (those with nasty sequences) are masked, I told MIRA to take every alignment there. Which in your case led to "a lot" of reads having *all* their alignments analysed and stored. 


[...]
I'm currently using version 2.39, I suppose I should update to 2.42


I've removed said "security feature" from the code, have a try at 2.9.43 :-)
Also, if you have time, please try with and without masking nasty repeats. I'm curious about how it behaves in your real world case and what you thing is better. To get MIRA going when masking is off, increase -SK:mmhr (5 should be enough). 

Regards,
  Bastien





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

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