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

[Hilmar Lapp]

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
>>
>>
>>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------