[Bioperl-l] loading yeast data failing...

[Angshu Kar]

Hi,

Could you please help me resolve the follwoing error?

I run:

./load_seqdatabase.pl --dbname=USBA --dbuser=postgres --format=fasta
--driver=Pg --pipeline="SeqProcessor::Accession" yeast_nrpep.fasta

The error:

Loading yeast_nrpep.fasta ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("gi|4261605|gb|AAD13905.1|S58126_11111111111111","gi|4261605|gb|AAD13905.1|S58126_11111111111111","gi|4261605|gb|AAD13905.1|S58126_11111111111111","Unknown
[Saccharomyces cerevisiae]","0","") FKs (19,<NULL>)
ERROR:  value too long for type character varying(40)
---------------------------------------------------
Could not store gi|4261605|gb|AAD13905.1|S58126_11111111111111:
------------- EXCEPTION  -------------
MSG: error while executing statement in
Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: ERROR:  current transaction
is aborted, commands ignored until end of transaction block
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store
/home/akar/local/perl//Bio/DB/Persistent/PersistentObject.pm:272
STACK (eval) ./load_seqdatabase.pl:621
STACK toplevel ./load_seqdatabase.pl:604

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

 at ./load_seqdatabase.pl line 634

Should I change the field lengths for accession, name and identifier to some
value >40 in the bioentry table?  What  should I change it to?

Thanks,
Angshu