[BioSQL-l] load_seqdatabase.pl warnings and errors
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
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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