[Genome] needLargeMem: Out of memory

[Galt Barber]

I don't think Helder is trying to align two entire genomes
(human and mouse)
to each other.  If that were so, then he needs blastz anyways.

Furthermore, though blat targets can be huge genomes,
blat queries cannot exceed a certain size, so the queries would have
to be broken up into chunks of 5-10k and then the final
results would need chaining with tools.  Somewhat complex.
As you pointed out, most users would be better off just
using our chains.

Perhaps Helder can tell us more about what he's
really trying to do?

-Galt


On Tue, 15 Apr 2008, Hiram Clawson wrote:

> Good Morning Helder:
>
> I would guess trying to use both the mm9 and hg18 genomes
> together would require about 16 Gb of memory, or thereabouts.
>
> You *may* be able to do one chromosome vs. one chromosome
> at a time.  For example chr1 vs. chr1 which would be the
> worst case.  Even that may be too much for a 2 Gb memory
> machine, I don't know.  Try chrM vs chrM and work up from
> there.
>
> Your input to blat can be the chr1.fa fasta files.  You do
> not need to convert each fasta file to a 2bit file unless
> you are trying to save disk space.
>
> You can also use the genome browser chain and net tracks
> between hg18 and mm9.  Those are better alignments than blat
> can produce all by itself.
>
> --Hiram
>
> Helder Nakaya wrote:
> > Hey Galt, thanks.
> >
> > I'm trying to load hg18 and mm9. I have already converted all
> > chromosome .fa files to one single hg18.2bit file (with FaToTwoBit).
> >
> > I'm running stand-alone blat. But I have tried to load sequence genome
> > with gfServer before run blat.
> >
> > If I split the genome by chromosomes, will the database be the
> > directory containing the chr.2bit files?
> >
> > Best,
> >
> > Helder
> >
> > 2008/4/15, Galt Barber <galt at soe.ucsc.edu>:
> >> It means you are out of memory.
> >>  #define ENOMEM 12
> >>
> >> Which genome are you trying to load?
> >> How big is it?
> >> Are you running stand-alone blat? or gfServer/gfClient?
> >> What does your command-line look like?
> >>
> >> Typically when people don't have enough RAM,
> >> we advise them to split the database of the genome
> >> by chromosome, and do one blat run per chrom.
> >>
> >> One then needs to use utilities like
> >> pslReps or pslCDnaFilter
> >> to combine the resulting psl result files.
> >>
> >> -Galt
> >>
> >>
> >> On Tue, 15 Apr 2008, Helder Nakaya wrote:
> >>
> >>> Hi,
> >>>
> >>> I'm new on this list and maybe this is not a novel question.
> >>>
> >>> I have instaled the blatSrc34 on my laptop (UBUNTU, system type:
> >>> 32-bit, processor: Intel(R) Core2 Duo CPU, T7250, 2GHz) with 2038MB
> >>> (RAM).
> >>>
> >>> When I try to run BLAT, it gives me this error message:
> >>> "needLargeMem: Out of memory - request size 158821425 bytes, errno: 12"
> >>>
> >>> I would like to know if someone has also had this problem and how do I solve it.
> >>>
> >>> I think I need to allocate dynamic memory in memalloc.c program but I
> >>> don't know how to do this.
> >>>
> >>> Cheers,
> >>>
> >>> Helder
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