[mira_talk] mmhr problem

I am having a problem running a de novo 454 est assembly.  Essentially it
tells me I have lots of megahubs, and I am trying to track down what these
are.  To do that I am trying to force it to go ahead with the assembly by
setting mmhr=1 but it always aborts anyways saying the ratio is greater than
0, even though I set it to max at 1.  I could be doing it wrong, heres what
I do:

mira  -fasta -project=Px -SK:mmhr=1  -job=denovo,est,draft,454

It then reports the skim parameters as:
  Parameters for SKIM algorithm (-SK):
    Number of threads (not)                     : 2

    Bases per hash (bph)                        : 16
    Hash save stepping (hss)                    : 8
    Percent required (pr)                       : 80
    Maximum hashes in memory (mhim)             : 15000000

    Max hits per read (mhpr)                    : 30
    Mask nasty repeats (mnr)                    : no
        Repeat threshold (rt)                   : 10
    Max. megahub ratio (mmhr)                   : 0

With the mmhr set back at 0.

It then goes on before aborting.

Is there a better way to find out what the megahub is?  My sequences aren't
paired-end and I set ssf_extract to trim an apporpriate number of bases on
the left to account for an adapter which I know is supposed to be there.

please advise,
thanks,
Clayton Coffman

University of Missouri

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