[Bioperl-l] Cont: load_ontology.pl crashes

Mikko Arvas Mikko.Arvas at vtt.fi
Fri Oct 29 09:04:31 EDT 2004

>Date: Fri, 29 Oct 2004 10:44:17 +0100
>To: bioperl-l at portal.open-bio.org
>From: Mikko Arvas <Mikko.Arvas at vtt.fi>
>Subject: load_ontology.pl crashes
>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?

I got it working fine though on a machine with much less resources, but 
which has a MySql 4.0.21 could that just be it?


Mikko Arvas
VTT Biotechnology

e-mail:            mikko.arvas at vtt.fi
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                       FIN-02044 VTT, Finland

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