[mira_talk] Re: MIRA run failing due to megahubs
- From: Jose Huguet Tapia <jch63@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 13:35:31 -0400
"But the point is not to overcome the error message and keep the crap in
the dataset but to either properly
clean the input data or to drop it and make the life easier to the
assembler. It is also faster so "forget
this possibility". ;-)"
depends if the 'crap" is real "crap" or is a real composition of a complex
genome. Of course depends the types of repeats that you have in your list.
On Wed, Jun 25, 2014 at 12:59 PM, Martin MOKREJŠ <mmokrejs@xxxxxxxxx> wrote:
> Jose Huguet Tapia wrote:
> > Hello Victoria,
> > I believe that you could set the megahubs limit to a 1.
>
> But the point is not to overcome the error message and keep the crap in
> the dataset but to either properly
> clean the input data or to drop it and make the life easier to the
> assembler. It is also faster so "forget
> this possibility". ;-)
>
> > add
> >
> > -SK:mmhr=1 (for 1 % megahub accepted)
> >
> > Which version are you using? I work with V 4.0. and I found that the
> megahub limit is set up to 90. I do not if this right. Maybe Bastien could
> have a suggestion. My case seems to be more dramatical!. I have more than
> 90
> > Thanks
> >
> > On Wed, Jun 25, 2014 at 11:36 AM, Offord, Victoria <vofford@xxxxxxxxx
> <mailto:vofford@xxxxxxxxx>> wrote:
> >
> > Hi, ____
> >
> > __ __
> >
> > My MIRA run on a parasite transcriptome keeps ending with:____
> >
> > __ __
> >
> > You have 0.1052271917% of your reads as megahubs.____
> >
> > You have set a maximum allowed ratio of: 0.0000000000____
> >
> > __ __
> >
> > Ending the assembly because the maximum ratio has been
> reached/surpassed.____
> >
> > Failure, wrapped MIRA process aborted.____
>
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