[BioSQL-l] Problems with load_seqdatabase and genbank files

[Hilmar Lapp]

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
>>> 
>> 
> 
>