[BioSQL-l] load_seqdatabase.pl warnings and errors

Tue May 19 08:17:32 UTC 2009

Hi

I'm using:

biosql-1.0.1

bioperl-db-1.5.2_100

bioperl-1.5.2_102

When I run load_seqdatabase.pl on about 3000 GenBank sequences, I get:

Loading fmd_180509.gbk ...

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("AY312586S1","32307407","AY312586","Foot-and-mouth disease virus O
isolate O/SKR/2000 S fragment, complete

1,9762)

Duplicate entry 'AY312586-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (324,3,4)

Duplicate entry '324-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("AY312586S2","32307408","AY312587","Foot-and-mouth disease virus O
isolate O/SKR/2000 L fragment, complete

1,9762)

Duplicate entry 'AY312587-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (323,3,4)

Duplicate entry '323-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","2") FKs (323,22,4)

Duplicate entry '323-22-4-2' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","3") FKs (323,15,4)

Duplicate entry '323-15-4-3' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("AY312588S1","32307403","AY312588","Foot-and-mouth disease virus O
isolate O/SKR/2002 S fragment, complete

1,9762)

Duplicate entry 'AY312588-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (326,3,4)

Duplicate entry '326-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("AY312588S2","32307404","AY312589","Foot-and-mouth disease virus O
isolate O/SKR/2002 L fragment, complete

1,9762)

Duplicate entry 'AY312589-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (325,3,4)

Duplicate entry '325-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","2") FKs (325,22,4)

Duplicate entry '325-22-4-2' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","3") FKs (325,15,4)

Duplicate entry '325-15-4-3' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("S87919S2","247466","S87923","L [foot-and-mouth disease virus FMDV,
strain CS8, Genomic RNA, 10 nt, segmen

1,9754)

Duplicate entry 'S87923-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (782,3,4)

Duplicate entry '782-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","2") FKs (782,13,4)

Duplicate entry '782-13-4-2' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("S87919S1","247464","S87919","L [foot-and-mouth disease virus FMDV,
strain CS8, Genomic RNA, 35 nt, segmen

1,9754)

Duplicate entry 'S87919-1-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
values were ("","1") FKs (781,3,4)

Duplicate entry '781-3-4-1' for key 2

---------------------------------------------------

-------------------- WARNING ---------------------

MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values
were ("","Direct Submission","Submitted (12-AUG-2004) National Center
for Biotechnology Information, NIH, 

C-E8D3CBBD80002FA1","1","8170","") FKs (<NULL>)

Duplicate entry 'CRC-E8D3CBBD80002FA1' for key 3

---------------------------------------------------

Could not store NC_011452:

------------- EXCEPTION  -------------

MSG: create: object (Bio::Annotation::Reference) failed to insert or to
be found by unique key

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:206

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:251

STACK Bio::DB::Persistent::PersistentObject::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/Persistent/PersistentObject.pm:271

STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/AnnotationCollectionAdaptor.pm:

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:214

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:251

STACK Bio::DB::Persistent::PersistentObject::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/Persistent/PersistentObject.pm:271

STACK Bio::DB::BioSQL::SeqAdaptor::store_children
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/SeqAdaptor.pm:224

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:214

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/BioSQL/BasePersistenceAdaptor.pm:251

STACK Bio::DB::Persistent::PersistentObject::store
/usr/users/bioinformatics/data/foot-and-mouth/bioperl-db-1.5.2_100/Bio/D
B/Persistent/PersistentObject.pm:271

STACK (eval) load_seqdatabase.pl:622

STACK toplevel load_seqdatabase.pl:604

--------------------------------------

 at load_seqdatabase.pl line 635

Any clues?

Thanks

Mick

Head of Bioinformatics
Institute for Animal Health
Compton
Berks
RG20 7NN
01635 578411 

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