[BioSQL-l] memory error while loading SwissProt into Oracle usingbioperl-db

[Richard HOLLAND]

These are two separate problems. 

(1) is caused by bad data in your SwissProt file - some of the records
in the file refer to journal articles but have not stated any authors.
The associated reference objects then do not get created, and neither do
their dbxrefs, causing integrity constraint errors elsewhere.

(2) means what it says, it's run out of memory! Your script appears to
be creating objects, persisting them to the database, but then keeping
them in memory afterwards either in the BioPerl-db cache or by keeping
its own references somewhere? (I'm not sure of the exact workings of
BioPerl-db here, Hilmar could you enlighten us?). How much memory is
your Oracle instance and other software using on that server? How much
is left for BioPerl?

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> Jana Bauckmann
> Sent: Tuesday, June 14, 2005 5:52 PM
> To: biosql-l at open-bio.org
> Subject: [BioSQL-l] memory error while loading SwissProt into 
> Oracle usingbioperl-db
> 
> 
> Hi,
> 
> I would like to load SwissProt data into my Oracle 9.2 database with
> BioSQL as schema using load_seqdatabase.pl from bioperl-db. 
> I've got two
> problems:
> 
> 1) I get many (about 1300) warnings stating integrity 
> constraint errors:
> 
> ORA-02291: integrity constraint (BIOSQL_SP.FKDBX_REF) 
> violated - parent
> key not found (DBD ERROR: OCIStmtExecute)
> 
> ORA-01400: cannot insert NULL into 
> ("BIOSQL_SP"."SG_REFERENCE"."AUTHORS")
> (DBD ERROR: OCIStmtExecute)
> 
> 2) The script stops after 2 hours (34500 tuples in table 
> BioEntry) with
> message: Out of memory!
> 
> I guess problem 1 causes problem 2. Is this reasonable or do 
> I have two
> separated problems?
> 
> I run Oracle and the load script on the same machine with:
> Suse Linux 9.0 (kernel 2.4.21-291-smp) with  12 GB RAM
> perl 5.8.1, built for i586-linux-thread-multi
> bioperl 1.4
> bioperl-db 0.1
> DBI 1.48
> DBD::Oracle 1.16
> Oracle 9.2
> BioSQL schema for Oracle (downloaded from 
> http://cvs.open-bio.org/ on 6th
> June 2005)
> 
> Thanks for any suggestions,
> Jana
> 
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