[Bioperl-l] FW: Load_ontology.pl warnings and exceptions
Law, Annie
Annie.Law at nrc-cnrc.gc.ca
Wed Jul 21 17:13:22 EDT 2004
Hi,
I made a silly mistake. I forgot to put an underscore in the line
--fmtargs "-defsfile,/root/bioperl-db/data/GO.defs"
It should be -defs_file NOT -defsfile. I now have no warining or
exceptions.
thanks
> -----Original Message-----
> From: Law, Annie
> Sent: Wednesday, July 21, 2004 2:50 PM
> To: 'bioperl-l at bioperl.org'
> Subject: Load_ontology.pl warnings and exceptions
>
>
> Hi,
>
> Previously, I used load_ontology.pl and got about 5
> exceptions or warnings. Recently, while using the same
> bioperl and bioperl-db Setups. I tried to use the same
> version of load_ontology.pl again with the latest information
> from GO ontology. Now it seems that I get about 90 warnings
> exceptions about 50 listed after ..terms and others listed
> after ...relationships during the run. I'm pretty sure that
> only the input to the scripts has changed. Is this a normal outcome?
>
> Are these warnings only a reflection of the source file and
> an annotation of work in progress or is there something that I
> Am missing? I wanted to eliminate the interference of
> previously existing data so I went and created a new
> database, loaded the Bioperl schema and used the
> load_ncbi_taxonomy.pl script then I used the load_ontology.pl script.
>
> Here is the output of the run. It seems to me that they are
> all complaints of duplicate entries. All of the bioperl is
> 1.4 and was installed around this past March.
>
> I would appreciate some insight.
> Thanks,
> Annie.
>
> Script started on Wed 21 Jul 2004 01:27:45 PM EDT
> > perl /root/bioperl-db/scripts/biosql/load_ontology.pl --dbuser=
> =user1 --dbpass=pass1 --dbname mydatabase --safe --computetc
> --noobsolete --names space "Gene Ontology" --format goflat
> --fmtargs "-defsfile,/root/bioperl-db/data/GO.defs" /ro
> oot/bioperl-db/data/function.ontology
> /root/bioperl-db/data/process.ontology /root/bioperl-db
> b/data/component.ontology Parsing input ... Loading ontology
> Gene Ontology:
> ... terms
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0001529","elastin","","") FKs (1) Duplicate
> entry 'elastin-1' for key 2
> ---------------------------------------------------
> Could not store GO:0001529 (elastin):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005581","collagen","","") FKs (1) Duplicate
> entry 'collagen-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005581 (collagen):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005676","condensin complex","","") FKs (1)
> Duplicate entry 'condensin complex-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005676 (condensin complex):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005699","kinetochore","","") FKs (1)
> Duplicate entry 'kinetochore-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005699 (kinetochore):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005716","synaptonemal complex","","") FKs
> (1) Duplicate entry 'synaptonemal complex-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005716 (synaptonemal complex):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005717","chromatin","","") FKs (1)
> Duplicate entry 'chromatin-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005717 (chromatin):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005718","nucleosome","","") FKs (1)
> Duplicate entry 'nucleosome-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005718 (nucleosome):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0005733","small nucleolar RNA","","") FKs
> (1) Duplicate entry 'small nucleolar RNA-1' for key 2
> ---------------------------------------------------
> Could not store GO:0005733 (small nucleolar RNA):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed,
> values were ("GO:0006326","bent DNA binding","","") FKs (1)
> Duplicate entry 'bent DNA binding-1' for key 2
> ---------------------------------------------------
> Could not store GO:0006326 (bent DNA binding):
>
> ------------- EXCEPTION -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert
> or to be found by unique key STACK
> Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> aptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:270
> STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
> STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
>
> --------------------------------------
>
>
>
>
>
>
More information about the Bioperl-l
mailing list