[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
>
>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
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?
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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