[BioSQL-l] problem loading sequences

[Kaustubh Patil]

Hi,

I am trying to load NCBI bacterial genomes into a BioSQL database, using the script from bioperl-db  package. I get error about duplicate entry. It will be very nice if you can point out the problem. The details are as follows.

Any help is appreciated.

Cheers,
kaustubh

The command I run;

bp_load_seqdatabase.pl --host XXX --dbname XXX --dbuser XXXl --dbpass XXX --format genbank --namespace genbank_bacteria */*.gbk

I get the following output;

Loading Acaryochloris_marina_MBIC11017/NC_009925.gbk ...
Loading Acaryochloris_marina_MBIC11017/NC_009926.gbk ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("","Direct Submission","Submitted (17-OCT-2007) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA","CRC-459492F4E0CAB94B","1","374161","") FKs (<NULL>)
Duplicate entry 'CRC-459492F4E0CAB94B' for key 3
---------------------------------------------------
Could not store NC_009926:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/local/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/local/bin/bp_load_seqdatabase.pl line 636