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

Hilmar Lapp hlapp at gmx.net
Thu Nov 30 18:31:41 EST 2006


Maybe Sendu can shed light on what might be happening here?

On Nov 30, 2006, at 5:19 PM, pelikan at cs.pitt.edu wrote:

> 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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> Bioperl-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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