[Bioperl-l] Error in loading into biosql database

[Siddhartha Basu]

Hi,
It was a multiple version problem. So i loaded everything freshly and 
the earlier errors have disappeared. But now it seems to be failing with 
different errors....

========================================================================
DBD::mysql::st execute failed: Duplicate entry 'Homo sapiens--' for key 
3 at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line 
564, <GEN0> line 310.

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SpeciesAdaptor (driver) failed, values 
were 
("Human","sapiens:Homo:Hominidae:Catarrhini:Primates:Eutheria:Mammalia:Euteleostomi:Vertebrata:Craniata:Chordata:Metazoa:Eukaryota","9606","Homo 
sapiens","-") FKs ()
Duplicate entry 'Homo sapiens--' for key 3
---------------------------------------------------

------------- EXCEPTION  -------------
MSG: Could not store P42655:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Species) failed to insert or to be found by 
unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:197
STACK Bio::DB::Persistent::PersistentObject::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:242
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) load_seqdatabase.pl:424
STACK toplevel load_seqdatabase.pl:423

--------------------------------------


STACK toplevel load_seqdatabase.pl:433

--------------------------------------

==========================================================================

This is the error i am getting while i tried to load the swissprot 
format of whole human proteome released by ebi. I am also getting 
similar kind of multiple errors even if i use the file for mouse 
proteome and the locuslink LL_tmpl file.

Any idea what's happening now.

siddhartha


Hilmar Lapp wrote:

> This means you're not running the before-singapore-change branch of  
> bioperl-db. The offending table only came in after that tag. Maybe a  
> multiple version / forgotten purge problem?
> 
>     -hilmar