[mira_talk] Re: should this assembly be taking several days?
- From: Corey Frazer <9ctf@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 03 Jul 2010 09:12:19 -0400
Hi Jeremiah,
Thanks for the response. Actually there was one contig that had almost
400x coverage that turned out to be 16S ribosomal sequence. Through all
the overcalls one could see that there were several different alleles
present.
Anyway, this is all so fascinating that I don't mind being hunched over
a computer during the beautiful Kingston summer.
Cheers
Corey
On Sat, 2010-07-03 at 00:26 -0400, Jeremiah Davie wrote:
> Hi Corey,
> I've noticed similar contigs when using gsAssembler. Generally,
> they turn out to be plasmid associated sequences or, more commonly,
> sequences coding for ribosomal RNAs. A quick blast search of the high
> coverage contig ends, say 1000 bp or so (if possible), can generally
> clue you in as to whether its rRNA or something more complicated.
> Given that Kingston is a lovely city, especially in the summer, I'm
> hoping for "not complicated" : )
> - Jeremiah
>
>
>
> On Jul 2, 2010, at 8:47 PM, Corey Frazer wrote:
>
> > Thanks Bastien (and Bharat)
> >
> > I'll increase the ram and give it another shot.
> >
> > I'm not sure how repetitive my bug is relative to others, but I did
> > notice that there were a few small contigs in the gsAssembler output
> > that were several times the average coverage.
> >
> > Cheers
> >
> > Corey
> >
> > On Sat, 2010-07-03 at 01:22 +0200, Bastien Chevreux wrote:
> >> On Freitag 02 Juli 2010 Corey Frazer wrote:
> >>> [...]
> >>> So, has something gone off the rails here, or am I just going to
> >>> have to
> >>> let it run?
> >>
> >> I think the problem is RAM: the machine is swapping itself to
> >> death, Obviously
> >> the miramem estimate was a bit wrong in this special case ...
> >> perhaps more
> >> repeats than "normal" in your genome?
> >>
> >> If you could find a machine with 8 or better 12 GiB, I think you'd
> >> see MIRA
> >> finishing within a couple of hours.
> >>
> >> Also, I suppose you are using 3.0.5. Try 3.1.15 (development
> >> version) which
> >> should use perhaps 20% less memory than the ... 8 GIB or so your
> >> process
> >> currently needs.
> >>
> >> http://www.chevreux.org/tmp/mira_3.1.15_dev_linux-gnu_x86_64_static.tar.bz2
> >>
> >> Or wait for after the week-end, when 3.2.0rc1 will be released.
> >>
> >> Regards,
> >> Bastien
> >>
> >
> > --
> > Corey Frazer
> >
> > PhD Candidate
> > PG Young Lab
> > Department of Biology
> > Queen's University
> > Kingston, ON
> > (613)-533-6000 ext77668
> >
> >
> > --
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> >
> >
>
>
--
Corey Frazer
PhD Candidate
PG Young Lab
Department of Biology
Queen's University
Kingston, ON
(613)-533-6000 ext77668
--
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