[Bioperl-l] Error with supplied lineages importing uniprot data

pelikan at cs.pitt.edu pelikan at cs.pitt.edu
Thu Nov 30 17:19:29 EST 2006


Hello all,

 I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows,
without Cygwin. The "make test"s have all completed without error. This
is my first time dealing with bioperl, so bear with me.

   I've successfully loaded the most recent taxonomy information using the
biosql-schema scripts. After this, I attempted to load the most recent
release of the uniprot flat file dataset with the following command:

load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass
********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat

I am subsequently greeted by many of the following errors:

Could not store Q7N3Q6:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Photorhabdus luminescens
subsp. laumondii'
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359
STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm:166
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:
STACK: Bio::DB::Persistent::PersistentObject::create
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2
STACK: Bio::DB::Persistent::PersistentObject::store
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271
STACK:
C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql\load_seqdatabase.pl:620
-----------------------------------------------------------

Can someone shed some light on why this may be taking place?

-Richard





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