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

[Rob S]

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!