From Gerben.Menschaert at UGent.be Mon Apr 24 09:43:12 2006 From: Gerben.Menschaert at UGent.be (Gerben Menschaert) Date: Mon, 24 Apr 2006 15:43:12 +0200 Subject: [BioSQL-l] BIOSQL on Oracle 10.1.0.3 needs an Oracle Patch Message-ID: <20060424134302.E7EE611631E@tarzan.ugent.be> Hello, Just for you information... If you're installing BIOSQL on Oracle 10.1.0.3 on Linux AS 2.1, you need to install the Oracle patch 3612581 (can be found on http://metalink.oracle.com). If not you will run into the following error, while testing the bioperl-db installation: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: error while executing statement in Bio::DB::BioSQL::PrimarySeqAdaptor::find_by_unique_key: ORA-00600: internal error code, arguments: [kpofdr-long], [], [], [], [], [], [], [] (DBD ERROR: error possibly near <*> indicator at char 138 in 'SELECT bioentry.oid, bioentry.name, bioentry.identifier, bioentry.accession, bioentry.description, bioentry.version, bioentry.db_oid FROM <*>bioentry WHERE db_oid = :p1 AND accession = :p2') STACK: Error::throw STACK: Bio::Root::Root::throw /src/bioperl/bioperl-live/Bio/Root/Root.pm:328 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855 STACK: t/03simpleseq.t:88 ----------------------------------------------------------- t/03simpleseq.....FAILED tests 29-59 Failed 31/59 tests, 47.46% okay If the patch is installed all tests are successful. I'm running perl v.5.8.0, Bioperl version 1.5.1 from CVS HEAD, Bioperl-db CVS HEAD, working on Biosql installed on Oracle 10.1.0.3 on Linux 2.1. AS. Regs, Gerben Menschaert From Gerben.Menschaert at UGent.be Mon Apr 24 10:52:35 2006 From: Gerben.Menschaert at UGent.be (Gerben Menschaert) Date: Mon, 24 Apr 2006 16:52:35 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl Message-ID: <20060424145226.A0D3345978E@tarzan.ugent.be> Hello, In the bioperl-db INSTALL file I saw that it's necessary to preload the ncbi taxonomy: #################################################### LOAD THE NCBI TAXONOMY You should pre-load the NCBI taxonomy database using the scripts/load_ncbi_taxonomy.pl script in the BioSQL package. Otherwise you will see errors from mis-parsed organisms when you attempt to load sequences. #################################################### I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the organism info correctly) taken care of in the load_seqdatabase.pl script now? Regs, Gerben Menschaert From cjfields at uiuc.edu Mon Apr 24 11:07:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 24 Apr 2006 10:07:24 -0500 Subject: [BioSQL-l] load_ncbi_taxonomy.pl In-Reply-To: <20060424145226.A0D3345978E@tarzan.ugent.be> Message-ID: <003401c667b0$cb2f7d70$15327e82@pyrimidine> The script is included with the biosql schema package: http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/?cvsroot=b iosql The reason it's included here instead of with bioperl-db is that the script, though perl, is not specifically used just for bioperl-db. It was designed to be independent of Bioperl, therefore can be used to load taxonomy for any BioSQL database. I think this is mentioned somewhere (in the INSTALL file or README, maybe) but I'm not sure... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l- > bounces at lists.open-bio.org] On Behalf Of Gerben Menschaert > Sent: Monday, April 24, 2006 9:53 AM > To: biosql-l at lists.open-bio.org > Subject: [BioSQL-l] load_ncbi_taxonomy.pl > > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to preload the > ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when you > attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the > organism info correctly) taken care of in the load_seqdatabase.pl script > now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From Marc.Logghe at DEVGEN.com Mon Apr 24 11:13:30 2006 From: Marc.Logghe at DEVGEN.com (Marc Logghe) Date: Mon, 24 Apr 2006 17:13:30 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl Message-ID: <0C528E3670D8CE4B8E013F6749231AA6746D17@ANTARESIA.be.devgen.com> Hi Gurb, It is a pretty old script that can be found in the biosql-schema repository. http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/scripts /?cvsroot=bioperl Good luck ! Cheers, ML Marc Logghe, PhD Expert Scientist Bioinformatics deVGen NV Technologiepark 30 B - 9052 Ghent-Zwijnaarde Tel. +32 9 324 24 83 Fax. +32 9 324 24 25 Web: www.devgen.com --- Disclaimer start --- This e-mail and any attachments thereto may contain information which is confidential and/or which is proprietary to the sender. Accordingly, this e-mail and any attachments thereto, as well as any and all information contained therein, are intended for the sole use of the recipient or recipients designated above. Any use of this e-mail, of any attachments thereto, of any and all information contained therein, and/or of any part(s) thereof (including, without limitation, total or partial reproduction, communication and/or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer. Thank you for your cooperation. --- Disclaimer end --- > -----Original Message----- > From: biosql-l-bounces at lists.open-bio.org > [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of > Gerben Menschaert > Sent: Monday, April 24, 2006 4:53 PM > To: biosql-l at lists.open-bio.org > Subject: [BioSQL-l] load_ncbi_taxonomy.pl > > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to > preload the ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when > you attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this > (parsing the organism info correctly) taken care of in the > load_seqdatabase.pl script now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > From arareko at campus.iztacala.unam.mx Mon Apr 24 11:34:09 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Mon, 24 Apr 2006 10:34:09 -0500 Subject: [BioSQL-l] load_ncbi_taxonomy.pl In-Reply-To: <20060424145226.A0D3345978E@tarzan.ugent.be> References: <20060424145226.A0D3345978E@tarzan.ugent.be> Message-ID: <444CEFF1.2050506@campus.iztacala.unam.mx> The script isn't included in bioperl-db, it's located in the scripts directory for the biosql-schema distribution. Regards, Mauricio. Gerben Menschaert wrote: > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to preload the ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when you > attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the > organism info correctly) taken care of in the load_seqdatabase.pl script > now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From Gerben.Menschaert at UGent.be Mon Apr 24 13:43:12 2006 From: Gerben.Menschaert at UGent.be (Gerben Menschaert) Date: Mon, 24 Apr 2006 15:43:12 +0200 Subject: [BioSQL-l] BIOSQL on Oracle 10.1.0.3 needs an Oracle Patch Message-ID: <20060424134302.E7EE611631E@tarzan.ugent.be> Hello, Just for you information... If you're installing BIOSQL on Oracle 10.1.0.3 on Linux AS 2.1, you need to install the Oracle patch 3612581 (can be found on http://metalink.oracle.com). If not you will run into the following error, while testing the bioperl-db installation: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: error while executing statement in Bio::DB::BioSQL::PrimarySeqAdaptor::find_by_unique_key: ORA-00600: internal error code, arguments: [kpofdr-long], [], [], [], [], [], [], [] (DBD ERROR: error possibly near <*> indicator at char 138 in 'SELECT bioentry.oid, bioentry.name, bioentry.identifier, bioentry.accession, bioentry.description, bioentry.version, bioentry.db_oid FROM <*>bioentry WHERE db_oid = :p1 AND accession = :p2') STACK: Error::throw STACK: Bio::Root::Root::throw /src/bioperl/bioperl-live/Bio/Root/Root.pm:328 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855 STACK: t/03simpleseq.t:88 ----------------------------------------------------------- t/03simpleseq.....FAILED tests 29-59 Failed 31/59 tests, 47.46% okay If the patch is installed all tests are successful. I'm running perl v.5.8.0, Bioperl version 1.5.1 from CVS HEAD, Bioperl-db CVS HEAD, working on Biosql installed on Oracle 10.1.0.3 on Linux 2.1. AS. Regs, Gerben Menschaert From Gerben.Menschaert at UGent.be Mon Apr 24 14:52:35 2006 From: Gerben.Menschaert at UGent.be (Gerben Menschaert) Date: Mon, 24 Apr 2006 16:52:35 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl Message-ID: <20060424145226.A0D3345978E@tarzan.ugent.be> Hello, In the bioperl-db INSTALL file I saw that it's necessary to preload the ncbi taxonomy: #################################################### LOAD THE NCBI TAXONOMY You should pre-load the NCBI taxonomy database using the scripts/load_ncbi_taxonomy.pl script in the BioSQL package. Otherwise you will see errors from mis-parsed organisms when you attempt to load sequences. #################################################### I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the organism info correctly) taken care of in the load_seqdatabase.pl script now? Regs, Gerben Menschaert From cjfields at uiuc.edu Mon Apr 24 15:07:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 24 Apr 2006 10:07:24 -0500 Subject: [BioSQL-l] load_ncbi_taxonomy.pl In-Reply-To: <20060424145226.A0D3345978E@tarzan.ugent.be> Message-ID: <003401c667b0$cb2f7d70$15327e82@pyrimidine> The script is included with the biosql schema package: http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/?cvsroot=b iosql The reason it's included here instead of with bioperl-db is that the script, though perl, is not specifically used just for bioperl-db. It was designed to be independent of Bioperl, therefore can be used to load taxonomy for any BioSQL database. I think this is mentioned somewhere (in the INSTALL file or README, maybe) but I'm not sure... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l- > bounces at lists.open-bio.org] On Behalf Of Gerben Menschaert > Sent: Monday, April 24, 2006 9:53 AM > To: biosql-l at lists.open-bio.org > Subject: [BioSQL-l] load_ncbi_taxonomy.pl > > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to preload the > ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when you > attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the > organism info correctly) taken care of in the load_seqdatabase.pl script > now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From Marc.Logghe at DEVGEN.com Mon Apr 24 15:13:30 2006 From: Marc.Logghe at DEVGEN.com (Marc Logghe) Date: Mon, 24 Apr 2006 17:13:30 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl Message-ID: <0C528E3670D8CE4B8E013F6749231AA6746D17@ANTARESIA.be.devgen.com> Hi Gurb, It is a pretty old script that can be found in the biosql-schema repository. http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/scripts /?cvsroot=bioperl Good luck ! Cheers, ML Marc Logghe, PhD Expert Scientist Bioinformatics deVGen NV Technologiepark 30 B - 9052 Ghent-Zwijnaarde Tel. +32 9 324 24 83 Fax. +32 9 324 24 25 Web: www.devgen.com --- Disclaimer start --- This e-mail and any attachments thereto may contain information which is confidential and/or which is proprietary to the sender. Accordingly, this e-mail and any attachments thereto, as well as any and all information contained therein, are intended for the sole use of the recipient or recipients designated above. Any use of this e-mail, of any attachments thereto, of any and all information contained therein, and/or of any part(s) thereof (including, without limitation, total or partial reproduction, communication and/or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer. Thank you for your cooperation. --- Disclaimer end --- > -----Original Message----- > From: biosql-l-bounces at lists.open-bio.org > [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of > Gerben Menschaert > Sent: Monday, April 24, 2006 4:53 PM > To: biosql-l at lists.open-bio.org > Subject: [BioSQL-l] load_ncbi_taxonomy.pl > > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to > preload the ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when > you attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this > (parsing the organism info correctly) taken care of in the > load_seqdatabase.pl script now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > From arareko at campus.iztacala.unam.mx Mon Apr 24 15:34:09 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Mon, 24 Apr 2006 10:34:09 -0500 Subject: [BioSQL-l] load_ncbi_taxonomy.pl In-Reply-To: <20060424145226.A0D3345978E@tarzan.ugent.be> References: <20060424145226.A0D3345978E@tarzan.ugent.be> Message-ID: <444CEFF1.2050506@campus.iztacala.unam.mx> The script isn't included in bioperl-db, it's located in the scripts directory for the biosql-schema distribution. Regards, Mauricio. Gerben Menschaert wrote: > Hello, > > In the bioperl-db INSTALL file I saw that it's necessary to preload the ncbi > taxonomy: > > #################################################### > LOAD THE NCBI TAXONOMY > You should pre-load the NCBI taxonomy database using the > scripts/load_ncbi_taxonomy.pl script in the BioSQL package. > Otherwise you will see errors from mis-parsed organisms when you > attempt to load sequences. > #################################################### > > I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the > organism info correctly) taken care of in the load_seqdatabase.pl script > now? > > Regs, > Gerben Menschaert > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM