[Bioperl-l] load_seqdatabase.pl error

Hilmar Lapp hlapp at gmx.net
Thu Sep 27 18:17:16 EDT 2007


Forrest,

have you preloaded the NCBI taxonomy as suggested in the BioSQL  
installation guidelines? SwissProt format has NCBI taxon IDs, and the  
code will try to use it to look up species and their lineage, rather  
than inserting the lineage from whatever BioPerl parses out of the  
sequence record.

	-hilmar

On Sep 27, 2007, at 3:41 AM, Forrest wrote:

> 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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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







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