[mira_talk] Re: Mira says "killed" as last word after being almost done
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 16 May 2011 13:14:35 -0400
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
48 GB ram
2 quad core 2.4 Ghz xeons
Fedora 14, using about 80% of ram.
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.
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?
Here is a bit of log, last 300 lines, more than ahppy to provide more:
http://pastebin.ca/2061695
Thanks everyone.
On Sun, May 15, 2011 at 7:25 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Sunday 15 May 2011 22:46:51 Adrian Pelin wrote:
>
> > Yes sorry about that, i started to use the stable version.... you know
>
> > because I thought stable is better and that is the case in most
>
> > programs.
>
>
> I think I'll soon need to make a stable 3.4, too much has changed since
> 3.2.1 stable.
>
>
> > But I am using .15 as .16 came out just today and my assembly
>
> > is running for 3 days now.
>
>
> .16 is so yesterday ... .17 is better (I know, too many versions in a short
> time frame, but I simply could not resist to use the week-end to get Ion
> Torrent done right ;-)
>
>
> B.
>
>
>
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