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

[Jana Bauckmann]

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