[maker-devel] Maker deep recursion leading to out of memory error

[Rob S]

After the bioperl upgrade, it has run overnight with no signs of
halting. Thanks Barry.
-r

On Oct 14, 11:41 am, Barry Moore <barry.mo... at genetics.utah.edu>
wrote:
> Rob,
>
> Not sure right off, but I see you've got bioperl 1.5.2.  The latest  
> version of MAKER requires bioperl 1.6 or higher.  As a starting point  
> I'd suggest getting the latest version of MAKER from here:http://www.yandell-lab.org/software/maker.html
>   and update to BioPerl 1.6.  If you're still having problems give us  
> some info about the nature of your assembly and more details about how  
> you are running MAKER (i.e. command line and control files).
>
> B
>
> On Oct 13, 2009, at 6:44 PM, Rob S wrote:
>
>
>
> > When running maker on a denovo genome assembly, Maker seems to exhaust
> > all the available memory by going into deep recursion. The following
> > error was produced after running Maker on an Altix XE cluster with
> > 15GB of memory. I have run a different genome assembly through Maker
> > and produced the same error.
> > The job was not run with MPI, but I suspect that the recursion will
> > consume all memory that is available to the application.
>
> > Does anybody know how to avoid the recursion/memory problem?
>
> > Widget::tblastx:
> > /opt/blast/2.2.20/bin/blastall -p tblastx -d /tmp/maker_acsicb/
> > 080611_sn15_aagi_cds.fas.fasta -i /tmp/maker_acsicb/rank0/
> > NODE_2_length_12288_cov_13.910726.0 -b 100000 -v 100000 -e 1e-10 -z
> > 1000 -Y 500000000 -a 8 -K 100 -U -F T -I -o /mnt/datafs/scratch/bi03/
> > rsyme/sn4-maker/sn4-contigs.maker.output/sn4-contigs_datastore/BD/30/
> > NODE_2_length_12288_cov_13.910726//
> > theVoid.NODE_2_length_12288_cov_13.910726/
> > NODE_2_length_12288_cov_13.910726.0.080611_sn15_aagi_cds.fas.tblastx.temp_dir
> > /
> > 080611_sn15_aagi_cds.fas.tblastx
> > #-------------------------------#
> > Deep recursion on subroutine "Bio::Search::HSP::GenericHSP::query"  
> > at /
> > opt/bioperl/1.5.2_102/lib/perl5/site_perl/5.8.8/Bio/Search/HSP/
> > GenericHSP.pm line 1311, <GEN72> line 3682.
> > Deep recursion on subroutine
> > "Bio::Search::HSP::GenericHSP::_query_seq_feature" at /opt/bioperl/
> > 1.5.2_102/lib/perl5/site_perl/5.8.8/Bio/Search/HSP/GenericHSP.pm line
> > 835, <GEN72> line 3682.
> > Out of memory!
>
> > _______________________________________________
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> > maker-de... at yandell-lab.org
> >http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
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