[Bioperl-l] load_ontology.pl crashes

[Hilmar Lapp]

Use --format interprosax. This will use the SAX-based parser in bioperl 
which consumes only a constant amount of memory. The older-generation 
interpro parser will consume huge amounts of memory and therefore crash 
on many systems.

	-hilmar

On Friday, October 29, 2004, at 02:44  AM, Mikko Arvas wrote:

> Hi,
>
> 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
> ....
> 10900
> 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?
>
> Cheers,
> mikko
> 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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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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