[Genome] needLargeMem: Out of memory

[Galt Barber]

If you were experimenting with gfServer earlier,
but are now wanting to use stand-alone blat instead,
then perhaps you might not have stopped the gfServer
processes? These could still be running and using up
memory that you need.  If so, do some sort of
process status to check, e.g.

 ps aux | grep gfServer

(unfortunately, the ps or process-status command is
Operating System-dependent and your exact commandline-params
for ps may be different)

if it shows gfServer is still running,
use the kill command to stop the gfServer processes.

Let me know when you sure that there are no gfServer processes
running any more now.

Then we can move on to using stand-alone blat.

-Galt


On Tue, 15 Apr 2008, 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
> > > _______________________________________________
> > > Genome maillist  -  Genome at soe.ucsc.edu
> > > http://www.soe.ucsc.edu/mailman/listinfo/genome
> > >
> >
>
>
> --
> ======================================================
>
>  Helder I. Nakaya, PhD
>  Laboratório de Análise de Expressão Gênica em Eucariotos
>  Instituto de Química, Departamento de Bioquímica.
>  Universidade de São Paulo. Brazil.
>  +55 11 3091-2173
>
> ======================================================
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>