[BioSQL-l] error loading uniprot release 49.6 into mysql

[s.rayner at att.net]

 Hello,
 
 I have been trying to upload the current release of uniprot (version 49.6) into 
 MySQL using the most current version of load_seqdatabase.pl from CVS  
 
 (# $Id: load_seqdatabase.pl,v 1.24 2006/01/19 21:34:29 lapp Exp $)
 
 I have tested the script on subsets of uniprot and it loads without problem, but 
 when i attempt to load the full dataset, i end up with the follow error....
 
 
 
 
 biowiv:/usr/lib/perl5/bioperl-db/scripts/biosql # perl load_seqdatabase.pl 
 --dbname uniprot --dbuser XXXX --dbpass XXXX --format swiss 
 /var/downloads/sequence/uniprot_sprot.dat
 Loading /var/downloads/sequence/uniprot_sprot.dat ...
 
 -------------------- WARNING ---------------------
 MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were 
 ("","","Submitted (NOV-2004) to the EMBL/GenBank/DDBJ 
 databases.","CRC-E7973FEA4B5611DC","","","") FKs (<NULL)
 Duplicate entry 'CRC-E7973FEA4B5611DC' for key 3
 ---------------------------------------------------
 Could not store Q5RFJ2:
 ------------- EXCEPTION  -------------
 MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found 
 by unique key
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:208
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/Persistent/PersistentObject.pm:272
 STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:219
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/Persistent/PersistentObject.pm:272
 STACK Bio::DB::BioSQL::SeqAdaptor::store_children 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/SeqAdaptor.pm:226
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store 
 /usr/lib/perl5/site_perl/5.8.7/Bio/DB/Persistent/PersistentObject.pm:272
 STACK (eval) load_seqdatabase.pl:620
 STACK toplevel load_seqdatabase.pl:602
 
 -------
 
 
 
 
 To create the biosql schema i used biosqldb-mysql.sql
 
 version info;
 -- $Id: biosqldb-mysql.sql,v 1.41 2005/04/18 05:21:38 lapp Exp $
 
 --------
 
 
 
 
 
 If i look at the data that has been created in the database, the first 
 1000 or so entries load successfully.  The offending record begins..
 
    ID   1433T_PONPY    STANDARD;      PRT;   245 AA.
    AC   Q5RFJ2; Q5RDK2;
 
 The script doesn't like Accession Number "Q5RFJ2", but the only other place it 
 shows up in the file is further down the same record as a "DR" entry.
 
    DR   SMR; Q5RFJ2; 1-230.
 
 I'm new to this and still trying to figure out the structure of all the tables.  
 Does anyone have any idea what is happening? 
 
 thanks for the help!