[Bioperl-l] Error with supplied lineages importing uniprot data

Chris Fields cjfields at uiuc.edu
Fri Dec 1 14:00:13 EST 2006


On Dec 1, 2006, at 11:12 AM, Sendu Bala wrote:

> pelikan at cs.pitt.edu wrote:
>> Hello all,
>>
>>  I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows,
>> without Cygwin. The "make test"s have all completed without error.  
>> This
>> is my first time dealing with bioperl, so bear with me.
>>
>>    I've successfully loaded the most recent taxonomy information  
>> using the
>> biosql-schema scripts. After this, I attempted to load the most  
>> recent
>> release of the uniprot flat file dataset with the following command:
>>
>> load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root - 
>> dbpass
>> ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat
>>
>> I am subsequently greeted by many of the following errors:
>>
>> Could not store Q7N3Q6:
>
> I extracted just Q7N3Q6 from
> ftp://ftp.expasy.org/databases/uniprot/current_release/ 
> knowledgebase/complete/uniprot_sprot.dat.gz
> and was able to load it in using load_seqdatabase.pl under linux  
> with no
> errors. If you make a file with just that sequence do you still get  
> the
> error?
>
> Is anyone else able to reproduce the problem?

I can reproduce on both WinXP and Mac OS X using the latest bioperl- 
db/bioperl-live and a BioSQL database preloaded with taxonomy.   
Notably the bug doesn't show up with a database lacking taxonomy,  
where no lookup is used (I guess).

Here's some overly verbose debugging (apologies):

Loading saved.flat ...
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::Tree::Tree
	attempting to load module Bio::DB::BioSQL::TreeAdaptor
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::Tree::TreeI
	attempting to load module Bio::DB::BioSQL::TreeIAdaptor
	attempting to load module Bio::DB::BioSQL::TreeAdaptor
attempting to load adaptor class for Bio::Tree::NodeI
	attempting to load module Bio::DB::BioSQL::NodeIAdaptor
	attempting to load module Bio::DB::BioSQL::NodeAdaptor
attempting to load adaptor class for Bio::Tree::TreeFunctionsI
	attempting to load module Bio::DB::BioSQL::TreeFunctionsIAdaptor
	attempting to load module Bio::DB::BioSQL::TreeFunctionsAdaptor
no adaptor found for class Bio::Tree::Tree
attempting to load adaptor class for Bio::DB::Taxonomy::list
	attempting to load module Bio::DB::BioSQL::listAdaptor
attempting to load adaptor class for Bio::DB::Taxonomy
	attempting to load module Bio::DB::BioSQL::TaxonomyAdaptor
no adaptor found for class Bio::DB::Taxonomy::list
attempting to load adaptor class for Bio::Annotation::Collection
	attempting to load module Bio::DB::BioSQL::CollectionAdaptor
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::Reference
	attempting to load module Bio::DB::BioSQL::ReferenceAdaptor
instantiating adaptor class Bio::DB::BioSQL::ReferenceAdaptor
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::Annotation::DBLink
	attempting to load module Bio::DB::BioSQL::DBLinkAdaptor
instantiating adaptor class Bio::DB::BioSQL::DBLinkAdaptor
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
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Tree::Tree
no adaptor found for class Bio::DB::Taxonomy::list
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
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::Tree::Tree
no adaptor found for class Bio::DB::Taxonomy::list
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
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::mysql::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 "Swiss-Prot" (namespace)
preparing INSERT statement: INSERT INTO biodatabase (name, authority)  
VALUES (?, ?)
BioNamespaceAdaptor::insert: binding column 1 to "Swiss- 
Prot" (namespace)
BioNamespaceAdaptor::insert: binding column 2 to "" (authority)
no adaptor found for class Bio::Tree::Tree
no adaptor found for class Bio::DB::Taxonomy::list
attempting to load driver for adaptor class  
Bio::DB::BioSQL::SpeciesAdaptor
Using Bio::DB::BioSQL::mysql::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 "141679" (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::mysql::BasePersistenceAdaptorDriver as driver  
peer for Bio::DB::BioSQL::SeqAdaptor
Could not store Q7N3Q6:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Photorhabdus  
luminescens subsp. laumondii'
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/cjfields/src/bioperl-live/Bio/ 
Root/Root.pm:359
STACK: Bio::Species::classification /Users/cjfields/src/bioperl-live/ 
Bio/Species.pm:166
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /Library/Perl/ 
5.8.6/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /Library/ 
Perl/5.8.6/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object / 
Library/Perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
Library/Perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
Library/Perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /Library/Perl/ 
5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create /Library/Perl/ 
5.8.6/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /Library/Perl/ 
5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /Library/Perl/ 
5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /Library/Perl/ 
5.8.6/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:620
-----------------------------------------------------------

at load_seqdatabase.pl line 633


chris


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