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

Angshu Kar angshu96 at gmail.com
Thu Dec 15 18:10:56 EST 2005 

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

Appreciate your guidance.

Thanks,
Angshu


On 12/13/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> Sure enough I should have checked whether you haven't responded already
> :-)
>
> On Dec 13, 2005, at 12:09 AM, Marc Logghe wrote:
>
> > Hi,
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at portal.open-bio.org
> >> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Angshu Kar
> >> Sent: Tuesday, December 13, 2005 2:57 AM
> >> To: bioperl-l
> >> Subject: [Bioperl-l] urgent:load_seqdatabase.pl doesn't seem
> >> to like fasta...
> >>
> >> Hi,
> >>
> >> This is the format that I've :
> >>
> >>> At1g01010.1 68414.m00001 no apical meristem (NAM) family protein
> >>> contains
> >> Pfam PF02365: No apical meristem (NAM) domain; sim ilar to
> >> NAC domain protein NAM GB: AAD17313 GI:4325282 from
> >> [Arabidopsis thaliana]
> >>
> >> And with regard to the following discussion:
> >>
> >> http://bioperl.org/pipermail/bioperl-l/2004-June/016198.html
> >>
> >> Could anyone please let me know whether any fixes have been
> >> done for this?
> >
> > Did you transfer the display_id to the accession_number slot ? See
> > recent discussions at
> > http://portal.open-bio.org/pipermail/bioperl-l/2005-August/019579.html
> > and links inside.
> > HTH,
> > Marc
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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