[BioSQL-l] Problems with load_seqdatabase and genbank files

Thu Aug 7 16:58:34 EDT 2003

problem solved,

it was an issue with the computer,

thanks

> > On Tue, 2003-08-05 at 21:58, Hilmar Lapp wrote:
> >> Albert, does the parser still barf on the swissprot file? I was able to run
> >> complete sprot and trembl a month ago and again now without the parser
> >> choking.
> >> 
> >>     -hilmar
> >> 
> >> On 6/11/03 5:40 AM, "albert vilella" <vilella at bio.ub.es> wrote:
> >> 
> >>> Ok,
> >>> 
> >>> I had downloaded the latest version of biosql-schema and bioperl-db with
> >>> cvs but I must had done something wrong because I didn't have the latest
> >>> version.
> >>> 
> >>> I downloaded and installed the tar.gz files linked from the viewcvs of
> >>> the project and there was no problem them.
> >>> 
> >>> Now I can populate the biosql database with genbank files.
> >>> 
> >>> I still have the same problem with swissprot files:
> >>> 
> >>> For example, if I try to enter a file with the first 3 entries of
> >>> sprot41.dat,
> >>> 
> >>> $ ./load_seqdatabase.pl /data/database/minisprot41.dat -format swiss
> >>> 
> >>> ------------- EXCEPTION  -------------
> >>> MSG: swissprot stream with no ID. Not swissprot in my book
> >>> STACK Bio::SeqIO::swiss::next_seq
> >>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/swiss.pm:179
> >>> STACK toplevel ./load_seqdatabase.pl:396
> >>>                
> >>> --------------------------------------
> >>> 
> >>> This happens with the lattest version of bioperl-live, bioperldb and
> >>> biosql-shema.
> >>> 
> >>> Thanks for you help,
> >>> 
> >>> Albert
> >>> 
> >>> On Tue, 2003-06-10 at 20:30, Hilmar Lapp wrote:
> >>>>> -----Original Message-----
> >>>>> From: albert vilella [mailto:vilella at bio.ub.es]
> >>>>> Sent: Tuesday, June 10, 2003 10:03 AM
> >>>>> To: biosql-l at open-bio.org
> >>>>> Subject: [BioSQL-l] Problems with load_seqdatabase and genbank files
> >>>>> 
> >>>>> 
> >>>>> Hello everybody,
> >>>>> 
> >>>>> I am trying to populate a database(biosql) with a little
> >>>>> GenBank sequence file using load_seqdatabase.pl (redhat linux).
> >>>>> 
> >>>>> I seems to be parsing the file correctly, but when it starts
> >>>>> to store the entries, it fails with the following error:
> >>>>> 
> >>>>> Loading /data/database/10014.gbk ...
> >>>>> DBD::mysql::st execute failed: Table 'biosql.term' doesn't
> >>>> 
> >>>> If you did instantiate the latest version of biosql then this message
> >>>> should not occur. It is a clear indication that you are trying to run
> >>>> off of an old schema version. If you type the following in the mysql
> >>>> shell, what do you see?
> >>>> 
> >>>> mysql> show tables like 'term%'; # should show 5 tables
> >>>> mysql> describe term;            # should show the table's
> >>>> columns
> >>>> mysql> describe ontology_term;   # should raise an error
> >>>> 
> >>>> It also seems you did not configure MySQL to enable the InnoDB table
> >>>> handler. Check the INSTALL document for how to do this. If you issue in
> >>>> mysql
> >>>> 
> >>>> mysql> show variables like 'have_innodb';
> >>>> 
> >>>> You should get 1 row and 'YES' in the right column if you have
> >>>> successfully enabled InnoDB.
> >>>> 
> >>>> -hilmar
> >>>> 
> >>>>> exist at 
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
> >>>>> line 903, <GEN0> line 599.
> >>>>> DBD::mysql::db rollback failed: Warning:  Some
> >>>>> non-transactional changed tables couldn't be rolled back at
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm
> >>>>> line 1649, <GEN0> line 599. Could not store NC_001321:
> >>>>> ------------- EXCEPTION  -------------
> >>>>> MSG: error while executing statement in
> >>>>> Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key:
> >>>>> Table 'biosql.term' doesn't exist STACK
> >>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:909
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:820
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:182
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:249
> >>>>> STACK Bio::DB::Persistent::PersistentObject::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> >>>>> ect.pm:266
> >>>>> STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollect
> >>>>> ionAdaptor.pm:218
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:214
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:249
> >>>>> STACK Bio::DB::Persistent::PersistentObject::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> >>>>> ect.pm:266
> >>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:226
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:214
> >>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> >>>>> aptor.pm:249
> >>>>> STACK Bio::DB::Persistent::PersistentObject::store
> >>>>> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> >>>>> ect.pm:266
> >>>>> STACK (eval) ./load_seqdatabase.pl:437
> >>>>> STACK toplevel ./load_seqdatabase.pl:421
> >>>>>  
> >>>>> --------------------------------------
> >>>>> 
> >>>>> I cvs'ed the last version of bioperl-db and biosql-schema, so
> >>>>> I'm using the latest version. Is the version that I should be using?
> >>>>> 
> >>>>> Any hint about what might be the problem?
> >>>>> 
> >>>>> Thanks in advance,
> >>>>> 
> >>>>> Albert
> >>>>> 
> >>>>> _______________________________________________
> >>>>> BioSQL-l mailing list
> >>>>> BioSQL-l at open-bio.org http://open-bio.org/mailman/listinfo/biosql-l
> >>>>> 
> >>>> 
> >>> 
> >>> 
> >> 
> >> 
> >