[BioSQL-l] Problems with load_seqdatabase and genbank files

[albert vilella]

Hello everybody,

I am trying to populate a database(biosql) with a little
GenBank sequence file using load_seqdatabase.pl (redhat linux).

I seems to be parsing the file correctly, but when it starts to store
the entries, it fails with the following error:

Loading /data/database/10014.gbk ...
DBD::mysql::st execute failed: Table 'biosql.term' doesn't exist at
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 903, <GEN0> line 599.
DBD::mysql::db rollback failed: Warning:  Some non-transactional changed
tables couldn't be rolled back at
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line 1649,
<GEN0> line 599.
Could not store NC_001321:
------------- EXCEPTION  -------------
MSG: error while executing statement in
Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key: Table
'biosql.term' doesn't exist
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:909
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:820
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:249
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:218
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:249
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK Bio::DB::BioSQL::SeqAdaptor::store_children
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:226
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:249
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) ./load_seqdatabase.pl:437
STACK toplevel ./load_seqdatabase.pl:421
 
--------------------------------------

I cvs'ed the last version of bioperl-db and biosql-schema, so I'm using
the latest version. Is the version that I should be using?

Any hint about what might be the problem?

Thanks in advance,

Albert