[mira_talk] Re: Mira says "killed" as last word after being almost done

Oh I see it did 3 Passes out of 5. So another day or two.

By the way, would a solid state drive increase speed of assemblies of mira
and other assemblers in general?

Adrian

On Mon, May 16, 2011 at 1:43 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On May 16, 2011, at 19:14 , Adrian Pelin wrote:
> > My hybrid,acurate,454,solexa,denovo assembly is on its 4th day and I was
> wondering if that is normal. Here is a bit of info:
> > 240,000 454 reads
> > 2000000 solexa pair-end reads
> > There are some contaminations of the DNA thought:( we have chunks of
> bacterial and fungal DNA and we are only interested in the Fungal
> mitochondrial DNA ~70-80kb.
>
> Oh, old friends of mine: mitochondria and chloroplasts. They are inherently
> difficult as most data sets I have seen up to know have a wildly varying
> coverage and, to complicate things, most of the time contain DNA from
> slightly different mitochondria/chloroplasts. Assembly hell par excellence.
>
> And then you have a small target (80kb) you sequence with tons and tons of
> reads. Ouch. Coverage >1000x ? MIRA will have a hard time.
>
> > We already have the genome assembled into 9 contigs, problem is that is
> still a lot, we would like to reduce it further to 4-5 contigs if possible
> and get different contigs from Mira algorithms.
> > Can anyone confirm that it is normal to have such a long wait time?
>
> That depends on the definition of "normal". However, as comparison, the run
> time for a small ~4.5mb bacterial genome with 800k 454bFLX reads and 3.5m
> Solexa reads is < 1 day (and that just because MIRA starts to build huge
> contigs of 1.5mb which slows down some things tremendously ... I'm working
> on that).
>
> MIRA *has* a hard time. That it takes so long is a sign that a lot of SNPs
> respectively repeat markers were found and disentangling them is a time
> consuming process. To asses where MIRA is:
>  grep "^Pass:" log_assembly.txt
> (or to whatever you redirected the output) and compare that to the number
> of passes with which MIRA is configured (see -AS:nop in the parameter
> section atop said file)
>
> The memory usage is less of a problem: MIRA just grabbed all it could / was
> allowed to load big tables and to less disk IO. No need to worry.
>
> B.
>
>
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