[Bioperl-l] load_ontology.pl crashes

Mikko Arvas Mikko.Arvas at vtt.fi
Fri Oct 29 05:44:17 EDT 2004


I am running Suse8.1, bioperl 1.4 w/ ontology modules updated from cvs, 
couple weeks old bioperl-db from cvs and mysql 3.23.52
on a desktop (2.4Ghz, 756Mb). I got NCBI taxon database and a few genomes 
inside biosql.

Otherwise things work fine, but when I am trying to load interpro the 
system crashes. for example:
 >nice -n 19 load_ontology --format interpro interpro.xml
and crashes.

How to proceed now, I am doing something stupid or is this just a too big 
job for my machine or is there a way to spilt the file somehow and feed it 
in pieces or can I somehow filter the interpro.xml file I actually need 
only fungi related data out of there?

Mikko Arvas
VTT Biotechnology

e-mail:            mikko.arvas at vtt.fi
tel:                 +358-(0)9-456 5827
mobile:           +358-(0)44-381 0502
fax:                +358-(0)9-455 2103
mail:               Tietotie 2, Espoo
                       P.O. Box 1500
                       FIN-02044 VTT, Finland

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