[Bioperl-l] load_seqdatabase error with a specific locus from genbank

Johann PELLET johann.pellet at inserm.fr
Wed Apr 1 06:14:25 EDT 2009


Hi all,

With the latest version of BioPerl and BioSQL, I have tried to insert  
entry from a GenBank file, which I have downloaded from the NCBI  
website (648 937 records)

After successfully loading ncbi_taxonomy i am getting following error  
message while loading sequences into database.

perl load_seqdatabase.pl gb_03-2009 -format genbank -driver Pg -dbname  
biosql


--------------------- WARNING ---------------------
MSG: The supplied lineage does not start near 'Human papillomavirus  
type 2c' (I was supplied 'Human papillomavirus - 2 |  
Alphapapillomavirus | Pa
pillomaviridae')

the script is not stopped until this entry: S67864

--------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed,  
values were ("1","19)","1","3") FKs (41914,<NULL>)
ERROR:  invalid input syntax for integer: "19)"

---------------------------------------------------
Could not store S67864:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in  
Bio::DB::BioSQL::LocationAdaptor::find_by_unique_key: ERROR:  current  
transaction is aborted, commands ig
nored until end of transaction block

STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm:357
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:970
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
Library/Perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK: Bio::DB::Persistent::PersistentObject::store /Library/Perl/ 
5.8.8/Bio/DB/Persistent/PersistentObject.pm:284
STACK: Bio::DB::BioSQL::SeqFeatureAdaptor::store_children /Library/ 
Perl/5.8.8/Bio/DB/BioSQL/SeqFeatureAdaptor.pm:291
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK: Bio::DB::Persistent::PersistentObject::store /Library/Perl/ 
5.8.8/Bio/DB/Persistent/PersistentObject.pm:284
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /Library/Perl/5.8.8/ 
Bio/DB/BioSQL/SeqAdaptor.pm:257
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /Library/Perl/ 
5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK: Bio::DB::Persistent::PersistentObject::store /Library/Perl/ 
5.8.8/Bio/DB/Persistent/PersistentObject.pm:284
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

  at load_seqdatabase.pl line 643

Any Idea?

Thanks in advance

Johann



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