[Bioperl-l] load_seqdatabase failed to run with .gbk
Angshu Kar
angshu96 at gmail.com
Fri Dec 16 13:22:40 EST 2005
Thanks Hilmar for your great inroads and suggestions. And yes, I'm in a
linux box...I would surely run the DBD::Pg tests and let you know the
results.
Thanks,
Angshu
On 12/16/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> So something kills your process - if it's not you or a sysadmin who
> doesn't like you then it is the OS. The OS would kill your process if
> it exceeds the per-process limits; on some systems (I thought you were
> on linux?) a segmentation fault or other compiled code or shared object
> problem could have the same symptom.
>
> So, either you have already a huge number of processes running and the
> OS thinks you reached the limit, or your machine is running out of
> memory (what's your hardware, and how did you configure Postgres), or
> there is a problem in a shared library being used (C runtime library?
> Pg client library? DBD::Pg shared object?). My #1 suspect would be the
> latter. Have you run the DBD::Pg tests? Was there any problem?
>
> Also, you still haven't commented on whether you ran the bioperl-db
> tests. It's hard to imagine that those would succeed but the script
> fails like this.
>
> -hilmar
>
> On Dec 16, 2005, at 7:27 AM, Angshu Kar wrote:
>
> > 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
> >>
> >>
> >>
> >
> > _______________________________________________
> > 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
> -------------------------------------------------------------
>
>
>
More information about the Bioperl-l
mailing list