[Bioperl-l] load_seqdatabase failed to run with .gbk

[Angshu Kar]

That was the entire  error msg when i used the debug option...and then
nothing got loaded in the tables...

On 12/16/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
>
>
> On 12/15/05 6:10 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:
>
> > Hi,
> >
> > The load_seqdatabase.pl failed to run with .gbk:
> >
> > akar at denton2 ~]$ ./load_seqdatabase.pl --dbname=USDA --dbuser=postgres
> > --format=genbank  --driver=Pg --debug  NC_003076.gbk
> > Loading NC_003076.gbk ...
> > attempting to load adaptor class for Bio::Seq::RichSeq
> >         attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
> > attempting to load adaptor class for Bio::Seq
> >         attempting to load module Bio::DB::BioSQL::SeqAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
> > attempting to load adaptor class for Bio::Species
> >         attempting to load module Bio::DB::BioSQL::SpeciesAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::SpeciesAdaptor
> > attempting to load adaptor class for Bio::Annotation::Collection
> >         attempting to load module Bio::DB::BioSQL::CollectionAdaptor
> > attempting to load adaptor class for Bio::Root::Root
> >         attempting to load module Bio::DB::BioSQL::RootAdaptor
> > attempting to load adaptor class for Bio::Root::RootI
> >         attempting to load module Bio::DB::BioSQL::RootIAdaptor
> >         attempting to load module Bio::DB::BioSQL::RootAdaptor
> > attempting to load adaptor class for Bio::AnnotationCollectionI
> >         attempting to load module
> > Bio::DB::BioSQL::AnnotationCollectionIAdaptor
> >         attempting to load module
> > Bio::DB::BioSQL::AnnotationCollectionAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::AnnotationCollectionAdaptor
> > attempting to load adaptor class for Bio::Annotation::TypeManager
> >         attempting to load module Bio::DB::BioSQL::TypeManagerAdaptor
> > no adaptor found for class Bio::Annotation::TypeManager
> > attempting to load adaptor class for Bio::Annotation::SimpleValue
> >         attempting to load module Bio::DB::BioSQL::SimpleValueAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::SimpleValueAdaptor
> > attempting to load adaptor class for Bio::Annotation::Comment
> >         attempting to load module Bio::DB::BioSQL::CommentAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::CommentAdaptor
> > attempting to load adaptor class for Bio::PrimarySeq
> >         attempting to load module Bio::DB::BioSQL::PrimarySeqAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::PrimarySeqAdaptor
> > attempting to load adaptor class for Bio::SeqFeature::Generic
> >         attempting to load module Bio::DB::BioSQL::GenericAdaptor
> > attempting to load adaptor class for Bio::SeqFeatureI
> >         attempting to load module Bio::DB::BioSQL::SeqFeatureIAdaptor
> >         attempting to load module Bio::DB::BioSQL::SeqFeatureAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::SeqFeatureAdaptor
> > attempting to load adaptor class for Bio::Location::Simple
> >         attempting to load module Bio::DB::BioSQL::SimpleAdaptor
> > attempting to load adaptor class for Bio::Location::Atomic
> >         attempting to load module Bio::DB::BioSQL::AtomicAdaptor
> > attempting to load adaptor class for Bio::LocationI
> >         attempting to load module Bio::DB::BioSQL::LocationIAdaptor
> >         attempting to load module Bio::DB::BioSQL::LocationAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::LocationAdaptor
> > attempting to load adaptor class for Bio::Location::Split
> >         attempting to load module Bio::DB::BioSQL::SplitAdaptor
> > attempting to load adaptor class for Bio::Location::Fuzzy
> >         attempting to load module Bio::DB::BioSQL::FuzzyAdaptor
> > no adaptor found for class Bio::Annotation::TypeManager
> > attempting to load adaptor class for BioNamespace
> >         attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
> > no adaptor found for class Bio::Annotation::TypeManager
> > attempting to load driver for adaptor class
> > Bio::DB::BioSQL::BioNamespaceAdaptor
> > attempting to load driver for adaptor class
> > Bio::DB::BioSQL::BasePersistenceAdaptor
> > Using Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver as driver peer
> for
> > Bio::DB::BioSQL::BioNamespaceAdaptor
> > preparing UK select statement: SELECT biodatabase.biodatabase_id,
> > biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = ?
> > BioNamespaceAdaptor: binding UK column 1 to "bioperl" (namespace)
> > preparing INSERT statement: INSERT INTO biodatabase (name, authority)
> VALUES
> > (?, ?)
> > BioNamespaceAdaptor::insert: binding column 1 to "bioperl" (namespace)
> > BioNamespaceAdaptor::insert: binding column 2 to "" (authority)
> > attempting to load driver for adaptor class
> Bio::DB::BioSQL::SpeciesAdaptor
> > Using Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver as driver peer for
> > Bio::DB::BioSQL::SpeciesAdaptor
> > preparing UK select statement: SELECT taxon_name.taxon_id, NULL, NULL,
> > taxon.ncbi_taxon_id, taxon_name.name, NULL FROM taxon, taxon_name WHERE
> > taxon.taxon_id = taxon_name.taxon_id AND name_class = ? AND
> ncbi_taxon_id =
> > ?
> > SpeciesAdaptor: binding UK column 1 to "scientific name" (name_class)
> > SpeciesAdaptor: binding UK column 2 to "3702" (ncbi_taxid)
> > prepare SELECT CLASSIFICATION: SELECT name.name, node.node_rank FROM
> taxon
> > node, taxon taxon, taxon_name name WHERE name.taxon_id = node.taxon_idAND
> > taxon.left_value BETWEEN node.left_value AND node.right_value AND
> > taxon.taxon_id = ? AND name.name_class = 'scientific name' ORDER BY
> > node.left_value
> > attempting to load driver for adaptor class Bio::DB::BioSQL::SeqAdaptor
> > attempting to load driver for adaptor class
> > Bio::DB::BioSQL::PrimarySeqAdaptor
> > attempting to load driver for adaptor class
> > Bio::DB::BioSQL::BasePersistenceAdaptor
> > Using Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver as driver peer
> for
> > Bio::DB::BioSQL::SeqAdaptor
> > preparing INSERT statement: INSERT INTO bioentry (name, identifier,
> > accession, description, version, division, biodatabase_id, taxon_id)
> VALUES
> > (?, ?, ?, ?, ?, ?, ?, ?)
> > SeqAdaptor::insert: binding column 1 to "NC_003076" (display_id)
> > SeqAdaptor::insert: binding column 2 to "30698605" (primary_id)
> > SeqAdaptor::insert: binding column 3 to "NC_003076" (accession_number)
> > SeqAdaptor::insert: binding column 4 to "Arabidopsis thaliana chromosome
> 5,
> > complete sequence." (desc)
> > SeqAdaptor::insert: binding column 5 to "4" (version)
> > SeqAdaptor::insert: binding column 6 to "PLN" (division)
> > SeqAdaptor::insert: binding column 7 to "14" (FK to
> > Bio::DB::Persistent::BioNamespace)
> > SeqAdaptor::insert: binding column 8 to "3702" (FK to Bio::Species)
> > attempting to load adaptor class for Biosequence
> >         attempting to load module Bio::DB::BioSQL::BiosequenceAdaptor
> > instantiating adaptor class Bio::DB::BioSQL::BiosequenceAdaptor
> > no adaptor found for class Bio::Annotation::TypeManager
> > attempting to load driver for adaptor class
> > Bio::DB::BioSQL::BiosequenceAdaptor
> > Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer for
> > Bio::DB::BioSQL::BiosequenceAdaptor
> > preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
> > bioentry_id = ?
> > Killed
>
> What does "Killed" mean?  Did you get an error?
>
> Sean
>
>
>