[BioSQL-l] Loading Genbank data

[Michael Acab]

I'm attempting to load Genbank data by loading *.gbk files but I'm having
trouble loading organisms which have more than one gbk file.  I can load
either the complete sequence or the plasmid but not both.  I get the
following error message.  Any help would be appreciated.


Loading
/home/shared/NCBI_genomes/curated/Bacteria/Agrobacterium_tumefaciens_C58_Cer
eon/NC_003063.gbk ...

------------- EXCEPTION  -------------
MSG: Could not store NC_003063:
------------- EXCEPTION  -------------
MSG: Invalid species name 'subsp. str.'
STACK Bio::Species::validate_species_name
/home/macab/lib/perl5/site_perl/5.6.1/Bio/Species.pm:306
STACK Bio::Species::classification
/home/macab/lib/perl5/site_perl/5.6.1/Bio/Species.pm:130
STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:
4
88
STACK Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/SpeciesAdaptor.pm:268
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAda
ptor.pm:1133
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersisten
ceAdaptor.pm:821
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.p
m
:180
STACK Bio::DB::Persistent::PersistentObject::create
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:
242
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.p
m
:167
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.p
m:
238
STACK Bio::DB::Persistent::PersistentObject::store
/home/macab/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:
266
[pathodb1] $ grep Invalid *.log
MSG: Invalid species name 'subsp. str.'
MSG: Invalid species name 'subsp. str.'
MSG: Invalid species name 'subsp. str.'
MSG: Invalid species name 'subsp. str.'
MSG: Invalid species name 'subsp. str.'
MSG: Invalid species name 'subsp. str.'


Thanks,
 
Michael R. Acab
Software Developer, Bioinformatics
The Brinkman Laboratory
Dept. of Molecular Biology and Biochemistry
Simon Fraser University
http://www.pathogenomics.sfu.ca/brinkman/
Tel: 604.291.5414
Fax: 604.291.5583