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

[Sean Davis]

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_id AND
> 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