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

[Barry Moore]

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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