[Bioperl-l] load_seqdatabase.pl error

Forrest forrest_zhang at 163.com
Thu Sep 27 03:41:44 EDT 2007


Hi, all
    I install the biosql, and bioperl-db. I want to import swissport data.
But the programe show some error as below:
============================================================================
===============================================
>perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver mysql
-namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
Loading /home/forrest/uniprot/uniprot_sprot.dat ...
Could not store Q6DAH5:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp.
atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium |
Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
Proteobacteria | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Species::classification
/usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:620
-----------------------------------------------------------

 at load_seqdatabase.pl line 633
============================================================================
===============================================

How can I solve it, please help me, Thank you.

Thanks
Forrest zhang





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