From gabrielle_doan at gmx.net Mon Sep 1 09:32:56 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Mon, 01 Sep 2008 15:32:56 +0200 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence Message-ID: <48BBEF08.8060402@gmx.net> Hi Richard, thanks a lot for your answer. I've changed the size of the rank in the BioSQL table seqfeature from smallint unsigned to int unsigned. So that the error messages because of the rank do not occur anymore. But now I'm facing an other problem. If I try to insert a new feature to human chromosome 1 and 2 into my database I get following message: org.hibernate.PropertyAccessException: Exception occurred inside getter of org.biojavax.bio.seq.SimpleRichSequence.stringSequence at org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:148) at org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:256) at org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:209) at org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:3581) at org.hibernate.event.def.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:167) at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:120) at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:196) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:76) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:145) ... 14 more Caused by: java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:2882) at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100) at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:572) at java.lang.StringBuffer.append(StringBuffer.java:320) at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTokenization.java:214) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenizeSymbolList(AlphabetManager.java:1460) at org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:102) at org.biojavax.bio.seq.DummyRichSequenceHandler.seqString(DummyRichSequenceHandler.java:115) at org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.seqString(BioSQLRichSequenceHandler.java:155) at org.biojavax.bio.seq.ThinRichSequence.seqString(ThinRichSequence.java:188) at org.biojavax.bio.seq.SimpleRichSequence.getStringSequence(SimpleRichSequence.java:77) ... 19 more I also had a conversation with Hilmar Lapp, who told me that there's possibly a bug in BioJava because the unique property does hold for the four elements bioentry_id, type_term_id, source_term_id and rank but it seems that BioJava always inkrements the rank for each new feature. Should I post a bug report? It would be very nice if you could help me. I am grateful for any hints. Thanks a lot. cheers Gabrielle -------- Original-Nachricht -------- Betreff: Re: [Biojava-l] Problems with adding miRNA to sequence Datum: Thu, 28 Aug 2008 23:45:35 +0100 Von: Richard Holland An: Gabrielle Doan CC: biojava-l at biojava.org Referenzen: <48B6B354.6010307 at gmx.net> Looks like your sequence has so many features that it exceeds the maximum permitted by BioSQL: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of range value adjusted for column 'rank' at row 1 Not sure what you can do about this other than go to the Feature table in your database and increase the maximum value allowed in the 'rank' column. cheers, Richard 2008/8/28 Gabrielle Doan : > > Hi all, > I would like to insert new features (miRNA) into my exitsting BioSQL > database. At the moment the database contains the chromosomes 1-22, X, Y > and MT downloaded from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/. And > now I have tried to add the information about miRNA from > http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl into my > database with following code: > > private void makeAFeature(String id, String chr, int startpos, > int endpos, Strand strand, float score, String gene) > throws ChangeVetoExceptionIllegalSymbolException > { > RichSequence rs = chromosomes.get(chr); > if (rs == null) { > rs = db.SearchForSequence(chr); > chromosomes.put(chr, rs); > } > RichFeature feat = RichFeature.Tools.makeEmptyFeature(); > feat.setName(id); > RichLocation rl = new SimpleRichLocation(new > > SimplePosition(startpos),new SimplePosition(endpos), > 1,strand); > feat.setLocation(rl); > try { > > feat.setTypeTerm(RichObjectFactory.getDefaultOntology() > .getOrCreateTerm("miRNA")); > feat.setType(feat.getTypeTerm().getName()); > } catch (InvalidTermException e) { > // TODO Auto-generated catch block > e.printStackTrace(); > } > feat.getAnnotation().setProperty("score", > Float.valueOf(score)); > feat.getAnnotation().setProperty("gene", gene); > feat.setParent(rs); > rs.getFeatureSet().add(feat); > } > > I successfully inserted the information for chromosome 3-22, X, Y and MT. > But when I try to deal with chromosome 1, 2 in the same way I get > following message: > > org.hibernate.exception.DataException: could not insert: [Feature] > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643) > at > org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51) > at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) > at > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298) > at > org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181) > at > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) > at > org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507) > at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) > at > org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218) > at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268) > at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) > at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) > at > org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296) > at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242) > at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) > at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) > at org.hibernate.engine.Cascade.cascade(Cascade.java:130) > at > org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131) > at > org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65) > at > org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) > at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) > at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) > at > org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) > at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) > at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) > at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) > Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of > range value adjusted for column 'rank' at row 1 > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at > com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129) > at > com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268) > at > org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33) > ... 32 more > > It would be very nice if someone could help me. I am grateful for any > hints. Thanks a lot. > > Cheers, > Gabrielle > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland Finance Director Eagle Genomics http://www.eaglegenomics.com/ From gabrielle_doan at gmx.net Mon Sep 1 09:38:28 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Mon, 01 Sep 2008 15:38:28 +0200 Subject: [BioSQL-l] [Fwd: Re: Increasing value of rank in table seqfeature] Message-ID: <48BBF054.50900@gmx.net> Hi Hilmar, you are right. I'm using BioJava to insert the features into my database. I'm suprised at the rank because in my source code I always set the rank to zero for each new feature I want to add to the human chromosome 1 and 2. But in my database the rank is always incremented. private void makeAFeature(String id, String chr, int startpos, int endpos, Strand strand, float score, String gene) throws ChangeVetoException, IllegalSymbolException { RichSequence rs = chromosomes.get(chr); if (rs == null) { rs = db.SearchForSequence(chr); chromosomes.put(chr, rs); } RichFeature feat = RichFeature.Tools.makeEmptyFeature(); // System.out.println("setParent " + rs.getName()); feat.setName(id); RichLocation rl = new SimpleRichLocation(new SimplePosition(startpos),new SimplePosition(endpos), 0, strand); feat.setLocation(rl); try { feat.setTypeTerm(RichObjectFactory.getDefaultOntology() .getOrCreateTerm("miRNA")); feat.setType(feat.getTypeTerm().getName()); } catch (InvalidTermException e) { // TODO Auto-generated catch block e.printStackTrace(); } feat.getAnnotation().setProperty("score", Float.valueOf(score)); feat.getAnnotation().setProperty("gene", gene); feat.setParent(rs); rs.getFeatureSet().add(feat); } It would be very nice if you could help me or give me any hint. Thanks a lot. cheers, Gabrielle -------- Original-Nachricht -------- Betreff: Re: [BioSQL-l] Increasing value of rank in table seqfeature Datum: Fri, 29 Aug 2008 10:45:26 -0400 Von: Hilmar Lapp An: Gabrielle Doan CC: biosql-l at lists.open-bio.org Referenzen: <48B7ED4A.5000008 at gmx.net> Hi Gabrielle, smallint can take values up to 65535 if unsigned. I can see that this can become a limitation if the bioentry to which the features belong is a whole chromosome. Note that the uniqueness constraint is not on bioentry (sequence) and rank. Instead, it is on the combination of bioentry (sequence), type term, source term, and rank. I.e., at present, with the smallint constraint, you can't have more than 65535 features of the same type and from the same source for a particular sequence. It's possible that the software you are using (Biojava?) increments the rank for every single feature, rather than resetting for each new combination of type and source. Is that what you are seeing? -hilmar On Aug 29, 2008, at 8:36 AM, Gabrielle Doan wrote: > Hi all, > I have a BioSQL database which contains several chromosomes and > features. And now I would like to insert chromosome 2 with some > miRNA as a new feature. I meet the problem that in the table > seqfeature the entry rank just can store smallint(5) unsigned > values. As fare as I know each rank has to be unique. If you want to > store many information this value will be excess quickly. Isn't it > better to increase this value? > > It would be very nice if someone could comment my suggestion. Thanks > a lot. > > Cheers, > Gabrielle > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Tue Sep 2 19:52:18 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Tue, 02 Sep 2008 16:52:18 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb Message-ID: <48BDD1B2.80407@berkeley.edu> Hi all, (sorry that I cross-posted this to the biopython lis, I only just realized I should get on the bioSQL list) I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get bioseqdb to work, and the biosql python scripts etc. However I can't get these directions to work in loading the taxonomy database into bioseqdb. I get: "Can't locate object method "connect" via package "DBI" " I double-checked to make sure I've got DBI in perl (see error message below) but that doesn't seem to help. Any help appreciated! Nick commands/returns: =========================== mws2:/bioinformatics/eg nick$ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 3 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com Built Jan 10 2008 11:08:33 Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page. mws2:/bioinformatics/eg nick$ sudo cpan DBI Password: CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Wed, 23 Jul 2008 10:02:50 GMT CPAN: LWP::UserAgent loaded ok (v5.810) CPAN: Time::HiRes loaded ok (v1.9711) Fetching with LWP: http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz CPAN: YAML loaded ok (v0.66) Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz ............................................................................DONE Fetching with LWP: http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz Database was generated on Mon, 01 Sep 2008 10:02:51 GMT ............................................................................DONE Fetching with LWP: http://ppm.activestate.com/CPAN/modules/03modlist.data.gz Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz ............................................................................DONE Going to write /usr/local/Metadata DBI is up to date (1.607). mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Can't locate object method "connect" via package "DBI" at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 323. mws2:/bioinformatics/eg nick$ =========================== Additional sleuthing: =========================== Based on some web advice on this general error I also did this: sudo cpan DBD::mysql ...which did install something that wasn't installed. But the same error resulted when the load_ncbi_taxonomy.pl script was run. =========================== Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not finding them in @INC or something doesn't seem to be the problem... (these commands return '1' if the module is successfully found) ============ perl -MDBD::mysql -e 'print 1' 1 perl -MDBI -e 'print 1' 1 ============ From hlapp at gmx.net Tue Sep 2 23:31:36 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 2 Sep 2008 23:31:36 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BDD1B2.80407@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> Message-ID: Hi Nick, this is working fine for me, using perl v5.8.8. You may have noticed that DBI does have a method 'connect'. Your perl reports to be 5.10, and to have been built for Mac OSX, yet it is a binary from ActiveState. Is my interpretation correct that you installed this on top of or in place of Mac OSX's native perl v5.8.8? Correspondingly, are you sure that 'perl' (which is what you are calling below), /usr/bin/perl (which is what the script executes), and cpan all are the same perl? If this is all correct and all the right platform, could you try and edit the following code (starting at line 323): my $dbh = DBI->connect($dsn, $user, $pass, { RaiseError => 0, AutoCommit => 1, PrintError => 0, } ) or die $DBI::errstr; by removing the 'or die $DBI::errstr' part. This would be hoping that it's an incompatibility for v5.10. BTW are you sure you need perl 5.10? You will encounter various perl software that has not been tested against it yet (though I think Bioperl has been fixed meanwhile to be compatible). -hilmar On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: > Hi all, > > (sorry that I cross-posted this to the biopython lis, I only just > realized I should get on the bioSQL list) > > > > I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy > ). I can get bioseqdb to work, and the biosql python scripts etc. > > However I can't get these directions to work in loading the taxonomy > database into bioseqdb. I get: "Can't locate object method > "connect" via package "DBI" " > > I double-checked to make sure I've got DBI in perl (see error > message below) but that doesn't seem to help. > > Any help appreciated! > Nick > > > > commands/returns: > =========================== > mws2:/bioinformatics/eg nick$ perl -v > > This is perl, v5.10.0 built for darwin-thread-multi-2level > (with 3 registered patches, see perl -V for more detail) > > Copyright 1987-2007, Larry Wall > > Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com > Built Jan 10 2008 11:08:33 > > Perl may be copied only under the terms of either the Artistic > License or the > GNU General Public License, which may be found in the Perl 5 source > kit. > > Complete documentation for Perl, including FAQ lists, should be > found on > this system using "man perl" or "perldoc perl". If you have access > to the > Internet, point your browser at http://www.perl.org/, the Perl Home > Page. > > > > > > > mws2:/bioinformatics/eg nick$ sudo cpan DBI > Password: > > CPAN: Storable loaded ok (v2.18) > Going to read /usr/local/Metadata > Database was generated on Wed, 23 Jul 2008 10:02:50 GMT > CPAN: LWP::UserAgent loaded ok (v5.810) > CPAN: Time::HiRes loaded ok (v1.9711) > Fetching with LWP: > http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz > CPAN: YAML loaded ok (v0.66) > Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz > ............................................................................DONE > Fetching with LWP: > http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz > Going to read /Users/nick/.cpan/sources/modules/ > 02packages.details.txt.gz > Database was generated on Mon, 01 Sep 2008 10:02:51 GMT > ............................................................................DONE > Fetching with LWP: > http://ppm.activestate.com/CPAN/modules/03modlist.data.gz > Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz > ............................................................................DONE > Going to write /usr/local/Metadata > DBI is up to date (1.607). > > > > > > > mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ > biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- > driver mysql --dbuser root --download true > > > Can't locate object method "connect" via package "DBI" at / > bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 323. > > mws2:/bioinformatics/eg nick$ > =========================== > > > > Additional sleuthing: > =========================== > Based on some web advice on this general error I also did this: > > sudo cpan DBD::mysql > > ...which did install something that wasn't installed. But the same > error resulted when the load_ncbi_taxonomy.pl script was run. > =========================== > > > Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not > finding them in @INC or something doesn't seem to be the problem... > > (these commands return '1' if the module is successfully found) > ============ > perl -MDBD::mysql -e 'print 1' > 1 > > perl -MDBI -e 'print 1' > 1 > ============ > > > > > > > > > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Tue Sep 2 23:57:02 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Tue, 02 Sep 2008 20:57:02 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: References: <48BDD1B2.80407@berkeley.edu> Message-ID: <48BE0B0E.6040604@berkeley.edu> Hi Hilmar! Thanks, that's a good thought. But I just tried running it on the default 5.8.6 (I have MacOX 10.4), same result: ========================================== mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' 1 mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' 1 mws2:~ nick$ perl5.8.6 -v This is perl, v5.8.6 built for darwin-thread-multi-2level (with 4 registered patches, see perl -V for more detail) Copyright 1987-2004, Larry Wall Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using `man perl' or `perldoc perl'. If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page. mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Can't locate object method "connect" via package "DBI" at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 323. ========================================== Just for kicks, I thought it might be a permission issue, so I tried it with sudo also, at least I got a different error: ================== mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Password: Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. ===================== (As for why I installed ActivePerl -- I don't remember, but it seemed like a good idea at the time when I was installing various packages and something or other requested or suggested the newer version. I was a total noob at the time. Still am, sorta...) Nick Hilmar Lapp wrote: > Hi Nick, > > this is working fine for me, using perl v5.8.8. You may have noticed > that DBI does have a method 'connect'. > > Your perl reports to be 5.10, and to have been built for Mac OSX, yet it > is a binary from ActiveState. Is my interpretation correct that you > installed this on top of or in place of Mac OSX's native perl v5.8.8? > Correspondingly, are you sure that 'perl' (which is what you are calling > below), /usr/bin/perl (which is what the script executes), and cpan all > are the same perl? > > If this is all correct and all the right platform, could you try and > edit the following code (starting at line 323): > > my $dbh = DBI->connect($dsn, > $user, > $pass, > { RaiseError => 0, > AutoCommit => 1, > PrintError => 0, > } > ) or die $DBI::errstr; > > by removing the 'or die $DBI::errstr' part. This would be hoping that > it's an incompatibility for v5.10. > > BTW are you sure you need perl 5.10? You will encounter various perl > software that has not been tested against it yet (though I think Bioperl > has been fixed meanwhile to be compatible). > > -hilmar > > On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: > >> Hi all, >> >> (sorry that I cross-posted this to the biopython lis, I only just >> realized I should get on the bioSQL list) >> >> >> >> I'm following the BioSQL tutorial at the biopython website >> (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get >> bioseqdb to work, and the biosql python scripts etc. >> >> However I can't get these directions to work in loading the taxonomy >> database into bioseqdb. I get: "Can't locate object method "connect" >> via package "DBI" " >> >> I double-checked to make sure I've got DBI in perl (see error message >> below) but that doesn't seem to help. >> >> Any help appreciated! >> Nick >> >> >> >> commands/returns: >> =========================== >> mws2:/bioinformatics/eg nick$ perl -v >> >> This is perl, v5.10.0 built for darwin-thread-multi-2level >> (with 3 registered patches, see perl -V for more detail) >> >> Copyright 1987-2007, Larry Wall >> >> Binary build 1002 [283697] provided by ActiveState >> http://www.ActiveState.com >> Built Jan 10 2008 11:08:33 >> >> Perl may be copied only under the terms of either the Artistic License >> or the >> GNU General Public License, which may be found in the Perl 5 source kit. >> >> Complete documentation for Perl, including FAQ lists, should be found on >> this system using "man perl" or "perldoc perl". If you have access to >> the >> Internet, point your browser at http://www.perl.org/, the Perl Home Page. >> >> >> >> >> >> >> mws2:/bioinformatics/eg nick$ sudo cpan DBI >> Password: >> >> CPAN: Storable loaded ok (v2.18) >> Going to read /usr/local/Metadata >> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >> CPAN: LWP::UserAgent loaded ok (v5.810) >> CPAN: Time::HiRes loaded ok (v1.9711) >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >> CPAN: YAML loaded ok (v0.66) >> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >> ............................................................................DONE >> >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >> Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz >> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >> ............................................................................DONE >> >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >> ............................................................................DONE >> >> Going to write /usr/local/Metadata >> DBI is up to date (1.607). >> >> >> >> >> >> >> mws2:/bioinformatics/eg nick$ >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> >> Can't locate object method "connect" via package "DBI" at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 323. >> >> mws2:/bioinformatics/eg nick$ >> =========================== >> >> >> >> Additional sleuthing: >> =========================== >> Based on some web advice on this general error I also did this: >> >> sudo cpan DBD::mysql >> >> ...which did install something that wasn't installed. But the same >> error resulted when the load_ncbi_taxonomy.pl script was run. >> =========================== >> >> >> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >> finding them in @INC or something doesn't seem to be the problem... >> >> (these commands return '1' if the module is successfully found) >> ============ >> perl -MDBD::mysql -e 'print 1' >> 1 >> >> perl -MDBI -e 'print 1' >> 1 >> ============ >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From hlapp at gmx.net Wed Sep 3 11:43:49 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 11:43:49 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BE0B0E.6040604@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> Message-ID: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Hi Nick, this is pretty weird. But the two different results between running with and without sudo strongly indicate that something's wrong with your perl installation setup. Specifically, DBI apparently isn't installed, and the DBI module that you are picking up without the sudo seems to be wrong or a corrupt one. You can ask perldoc for the full path to the module using the -l argument: $ perldoc -l DBI $ sudo perldoc -l DBI $ /usr/bin/perldoc -l DBI $ sudo /usr/bin/perldoc -l DBI should all yield the same result, and the following should, too: $ perl -e 'use DBI; $dbh=DBI- >connect("dbi:mysql:database=test","","");' w/ and w/o using the full path, w/ and w/o prepending sudo. Is that what you are seeing? -hilmar On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > Hi Hilmar! > > Thanks, that's a good thought. But I just tried running it on the > default 5.8.6 (I have MacOX 10.4), same result: > > > ========================================== > mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' > 1 > > mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' > 1 > > mws2:~ nick$ perl5.8.6 -v > > This is perl, v5.8.6 built for darwin-thread-multi-2level > (with 4 registered patches, see perl -V for more detail) > > Copyright 1987-2004, Larry Wall > > Perl may be copied only under the terms of either the Artistic > License or the > GNU General Public License, which may be found in the Perl 5 source > kit. > > Complete documentation for Perl, including FAQ lists, should be > found on > this system using `man perl' or `perldoc perl'. If you have access > to the > Internet, point your browser at http://www.perl.org/, the Perl Home > Page. > > > mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- > dbuser root --download true > > Can't locate object method "connect" via package "DBI" at / > bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 323. > ========================================== > > > Just for kicks, I thought it might be a permission issue, so I tried > it with sudo also, at least I got a different error: > > ================== > mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- > dbuser root --download true > > Password: > > Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/ > 5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/ > Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/ > Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/ > Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/ > 5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 / > Library/Perl/5.8.1 .) at /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl line 195. > > BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/ > biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. > ===================== > > > (As for why I installed ActivePerl -- I don't remember, but it > seemed like a good idea at the time when I was installing various > packages and something or other requested or suggested the newer > version. I was a total noob at the time. Still am, sorta...) > > Nick > > > Hilmar Lapp wrote: >> Hi Nick, >> this is working fine for me, using perl v5.8.8. You may have >> noticed that DBI does have a method 'connect'. >> Your perl reports to be 5.10, and to have been built for Mac OSX, >> yet it is a binary from ActiveState. Is my interpretation correct >> that you installed this on top of or in place of Mac OSX's native >> perl v5.8.8? Correspondingly, are you sure that 'perl' (which is >> what you are calling below), /usr/bin/perl (which is what the >> script executes), and cpan all are the same perl? >> If this is all correct and all the right platform, could you try >> and edit the following code (starting at line 323): >> my $dbh = DBI->connect($dsn, >> $user, >> $pass, >> { RaiseError => 0, >> AutoCommit => 1, >> PrintError => 0, >> } >> ) or die $DBI::errstr; >> by removing the 'or die $DBI::errstr' part. This would be hoping >> that it's an incompatibility for v5.10. >> BTW are you sure you need perl 5.10? You will encounter various >> perl software that has not been tested against it yet (though I >> think Bioperl has been fixed meanwhile to be compatible). >> -hilmar >> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>> Hi all, >>> >>> (sorry that I cross-posted this to the biopython lis, I only just >>> realized I should get on the bioSQL list) >>> >>> >>> >>> I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy >>> ). I can get bioseqdb to work, and the biosql python scripts etc. >>> >>> However I can't get these directions to work in loading the >>> taxonomy database into bioseqdb. I get: "Can't locate object >>> method "connect" via package "DBI" " >>> >>> I double-checked to make sure I've got DBI in perl (see error >>> message below) but that doesn't seem to help. >>> >>> Any help appreciated! >>> Nick >>> >>> >>> >>> commands/returns: >>> =========================== >>> mws2:/bioinformatics/eg nick$ perl -v >>> >>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>> (with 3 registered patches, see perl -V for more detail) >>> >>> Copyright 1987-2007, Larry Wall >>> >>> Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com >>> Built Jan 10 2008 11:08:33 >>> >>> Perl may be copied only under the terms of either the Artistic >>> License or the >>> GNU General Public License, which may be found in the Perl 5 >>> source kit. >>> >>> Complete documentation for Perl, including FAQ lists, should be >>> found on >>> this system using "man perl" or "perldoc perl". If you have >>> access to the >>> Internet, point your browser at http://www.perl.org/, the Perl >>> Home Page. >>> >>> >>> >>> >>> >>> >>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>> Password: >>> >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /usr/local/Metadata >>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>> CPAN: LWP::UserAgent loaded ok (v5.810) >>> CPAN: Time::HiRes loaded ok (v1.9711) >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>> CPAN: YAML loaded ok (v0.66) >>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>> ............................................................................DONE >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>> Going to read /Users/nick/.cpan/sources/modules/ >>> 02packages.details.txt.gz >>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>> ............................................................................DONE >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>> ............................................................................DONE >>> Going to write /usr/local/Metadata >>> DBI is up to date (1.607). >>> >>> >>> >>> >>> >>> >>> mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ >>> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >>> driver mysql --dbuser root --download true >>> >>> >>> Can't locate object method "connect" via package "DBI" at / >>> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >>> load_ncbi_taxonomy.pl line 323. >>> >>> mws2:/bioinformatics/eg nick$ >>> =========================== >>> >>> >>> >>> Additional sleuthing: >>> =========================== >>> Based on some web advice on this general error I also did this: >>> >>> sudo cpan DBD::mysql >>> >>> ...which did install something that wasn't installed. But the >>> same error resulted when the load_ncbi_taxonomy.pl script was run. >>> =========================== >>> >>> >>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >>> finding them in @INC or something doesn't seem to be the problem... >>> >>> (these commands return '1' if the module is successfully found) >>> ============ >>> perl -MDBD::mysql -e 'print 1' >>> 1 >>> >>> perl -MDBI -e 'print 1' >>> 1 >>> ============ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > ==================================================== > Nicholas J. Matzke > Ph.D. student, Graduate Student Researcher > Huelsenbeck Lab > Center for Theoretical Evolutionary Genomics > 4151 VLSB (Valley Life Sciences Building) > Department of Integrative Biology > University of California, Berkeley > > Lab websites: > http://ib.berkeley.edu/people/lab_detail.php?lab=54 > http://fisher.berkeley.edu/cteg/hlab.html > Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 > Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html > Lab phone: 510-643-6299 > Dept. fax: 510-643-6264 > Cell phone: 510-301-0179 > Email: matzke at berkeley.edu > > Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, > Ecology > VLSB 2013, Monday 1-1:30 (some TA there for all hours during work > week) > > Mailing address: > Department of Integrative Biology > 3060 VLSB #3140 > Berkeley, CA 94720-3140 > ==================================================== > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Sep 3 13:09:28 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Sep 2008 12:09:28 -0500 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Message-ID: <507AE529-1D58-44C9-A077-6A70A66DB5D3@illinois.edu> I'll give it a try; I have a locally built perl 5.10 on my laptop (Mac OS X). I know bioperl and bioperl-db work fine with perl 5.10, so maybe it is something with the script that is tripping things up. Maybe indirect object syntax ('new Class' instead of 'Class->new()')? The error looks similar to problems we have seen in the past which resolved when switching to the latter. chris On Sep 3, 2008, at 10:43 AM, Hilmar Lapp wrote: > Hi Nick, > > this is pretty weird. But the two different results between running > with and without sudo strongly indicate that something's wrong with > your perl installation setup. Specifically, DBI apparently isn't > installed, and the DBI module that you are picking up without the > sudo seems to be wrong or a corrupt one. > > You can ask perldoc for the full path to the module using the -l > argument: > > $ perldoc -l DBI > $ sudo perldoc -l DBI > $ /usr/bin/perldoc -l DBI > $ sudo /usr/bin/perldoc -l DBI > > should all yield the same result, and the following should, too: > > $ perl -e 'use DBI; $dbh=DBI- > >connect("dbi:mysql:database=test","","");' > > w/ and w/o using the full path, w/ and w/o prepending sudo. > > Is that what you are seeing? > > -hilmar > > On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > >> Hi Hilmar! >> >> Thanks, that's a good thought. But I just tried running it on the >> default 5.8.6 (I have MacOX 10.4), same result: >> >> >> ========================================== >> mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -v >> >> This is perl, v5.8.6 built for darwin-thread-multi-2level >> (with 4 registered patches, see perl -V for more detail) >> >> Copyright 1987-2004, Larry Wall >> >> Perl may be copied only under the terms of either the Artistic >> License or the >> GNU General Public License, which may be found in the Perl 5 source >> kit. >> >> Complete documentation for Perl, including FAQ lists, should be >> found on >> this system using `man perl' or `perldoc perl'. If you have access >> to the >> Internet, point your browser at http://www.perl.org/, the Perl Home >> Page. >> >> >> mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ >> scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- >> dbuser root --download true >> >> Can't locate object method "connect" via package "DBI" at / >> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >> load_ncbi_taxonomy.pl line 323. >> ========================================== >> >> >> Just for kicks, I thought it might be a permission issue, so I >> tried it with sudo also, at least I got a different error: >> >> ================== >> mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/ >> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >> driver mysql --dbuser root --download true >> >> Password: >> >> Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/ >> 5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 / >> Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 / >> Library/Perl /Network/Library/Perl/5.8.6/darwin-thread- >> multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl / >> System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/ >> Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /bioinformatics/ >> pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. >> >> BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/ >> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. >> ===================== >> >> >> (As for why I installed ActivePerl -- I don't remember, but it >> seemed like a good idea at the time when I was installing various >> packages and something or other requested or suggested the newer >> version. I was a total noob at the time. Still am, sorta...) >> >> Nick >> >> >> Hilmar Lapp wrote: >>> Hi Nick, >>> this is working fine for me, using perl v5.8.8. You may have >>> noticed that DBI does have a method 'connect'. >>> Your perl reports to be 5.10, and to have been built for Mac OSX, >>> yet it is a binary from ActiveState. Is my interpretation correct >>> that you installed this on top of or in place of Mac OSX's native >>> perl v5.8.8? Correspondingly, are you sure that 'perl' (which is >>> what you are calling below), /usr/bin/perl (which is what the >>> script executes), and cpan all are the same perl? >>> If this is all correct and all the right platform, could you try >>> and edit the following code (starting at line 323): >>> my $dbh = DBI->connect($dsn, >>> $user, >>> $pass, >>> { RaiseError => 0, >>> AutoCommit => 1, >>> PrintError => 0, >>> } >>> ) or die $DBI::errstr; >>> by removing the 'or die $DBI::errstr' part. This would be hoping >>> that it's an incompatibility for v5.10. >>> BTW are you sure you need perl 5.10? You will encounter various >>> perl software that has not been tested against it yet (though I >>> think Bioperl has been fixed meanwhile to be compatible). >>> -hilmar >>> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>>> Hi all, >>>> >>>> (sorry that I cross-posted this to the biopython lis, I only just >>>> realized I should get on the bioSQL list) >>>> >>>> >>>> >>>> I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy >>>> ). I can get bioseqdb to work, and the biosql python scripts etc. >>>> >>>> However I can't get these directions to work in loading the >>>> taxonomy database into bioseqdb. I get: "Can't locate object >>>> method "connect" via package "DBI" " >>>> >>>> I double-checked to make sure I've got DBI in perl (see error >>>> message below) but that doesn't seem to help. >>>> >>>> Any help appreciated! >>>> Nick >>>> >>>> >>>> >>>> commands/returns: >>>> =========================== >>>> mws2:/bioinformatics/eg nick$ perl -v >>>> >>>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>>> (with 3 registered patches, see perl -V for more detail) >>>> >>>> Copyright 1987-2007, Larry Wall >>>> >>>> Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com >>>> Built Jan 10 2008 11:08:33 >>>> >>>> Perl may be copied only under the terms of either the Artistic >>>> License or the >>>> GNU General Public License, which may be found in the Perl 5 >>>> source kit. >>>> >>>> Complete documentation for Perl, including FAQ lists, should be >>>> found on >>>> this system using "man perl" or "perldoc perl". If you have >>>> access to the >>>> Internet, point your browser at http://www.perl.org/, the Perl >>>> Home Page. >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>>> Password: >>>> >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /usr/local/Metadata >>>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>>> CPAN: LWP::UserAgent loaded ok (v5.810) >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>>> CPAN: YAML loaded ok (v0.66) >>>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>>> ............................................................................DONE >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>>> Going to read /Users/nick/.cpan/sources/modules/ >>>> 02packages.details.txt.gz >>>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>>> ............................................................................DONE >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>>> ............................................................................DONE >>>> Going to write /usr/local/Metadata >>>> DBI is up to date (1.607). >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ >>>> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >>>> driver mysql --dbuser root --download true >>>> >>>> >>>> Can't locate object method "connect" via package "DBI" at / >>>> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >>>> load_ncbi_taxonomy.pl line 323. >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> =========================== >>>> >>>> >>>> >>>> Additional sleuthing: >>>> =========================== >>>> Based on some web advice on this general error I also did this: >>>> >>>> sudo cpan DBD::mysql >>>> >>>> ...which did install something that wasn't installed. But the >>>> same error resulted when the load_ncbi_taxonomy.pl script was run. >>>> =========================== >>>> >>>> >>>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. >>>> not finding them in @INC or something doesn't seem to be the >>>> problem... >>>> >>>> (these commands return '1' if the module is successfully found) >>>> ============ >>>> perl -MDBD::mysql -e 'print 1' >>>> 1 >>>> >>>> perl -MDBI -e 'print 1' >>>> 1 >>>> ============ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> ==================================================== >> Nicholas J. Matzke >> Ph.D. student, Graduate Student Researcher >> Huelsenbeck Lab >> Center for Theoretical Evolutionary Genomics >> 4151 VLSB (Valley Life Sciences Building) >> Department of Integrative Biology >> University of California, Berkeley >> >> Lab websites: >> http://ib.berkeley.edu/people/lab_detail.php?lab=54 >> http://fisher.berkeley.edu/cteg/hlab.html >> Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 >> Lab personal page: http://fisher.berkeley.edu/cteg/members/ >> matzke.html >> Lab phone: 510-643-6299 >> Dept. fax: 510-643-6264 >> Cell phone: 510-301-0179 >> Email: matzke at berkeley.edu >> >> Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, >> Ecology >> VLSB 2013, Monday 1-1:30 (some TA there for all hours during work >> week) >> >> Mailing address: >> Department of Integrative Biology >> 3060 VLSB #3140 >> Berkeley, CA 94720-3140 >> ==================================================== >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From matzke at berkeley.edu Wed Sep 3 14:16:19 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 11:16:19 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Message-ID: <48BED473.6070006@berkeley.edu> Hmm, I think you are onto something here...here is what I get with those commands: ========================================== mws2:~ nick$ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 3 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com Built Jan 10 2008 11:08:33 mws2:~ nick$ perldoc -V Perldoc v3.14_02, under perl v5.010000 for darwin mws2:~ nick$ perldoc -l DBI /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm mws2:~ nick$ sudo perldoc -l DBI Password: /usr/local/ActivePerl-5.10/site/lib/DBI.pm mws2:~ nick$ /usr/bin/perldoc -l DBI /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm mws2:~ nick$ sudo /usr/bin/perldoc -l DBI No documentation found for "DBI". mws2:~ nick$ perl -e 'use DBI; $dbh=DBI->connect("dbi:mysql:database=test","","");' Can't locate object method "connect" via package "DBI" (perhaps you forgot to load "DBI"?) at -e line 1. mws2:~ nick$ sudo perl -e 'use DBI; $dbh=DBI->connect("dbi:mysql:database=test","","");' [no text returned, so I guess this cmd worked] ========================================== Suggestions about what to do based on this? Thanks again! Nick Hilmar Lapp wrote: > Hi Nick, > > this is pretty weird. But the two different results between running with > and without sudo strongly indicate that something's wrong with your perl > installation setup. Specifically, DBI apparently isn't installed, and > the DBI module that you are picking up without the sudo seems to be > wrong or a corrupt one. > > You can ask perldoc for the full path to the module using the -l argument: > > $ perldoc -l DBI > $ sudo perldoc -l DBI > $ /usr/bin/perldoc -l DBI > $ sudo /usr/bin/perldoc -l DBI > > should all yield the same result, and the following should, too: > > $ perl -e 'use DBI; > $dbh=DBI->connect("dbi:mysql:database=test","","");' > > w/ and w/o using the full path, w/ and w/o prepending sudo. > > Is that what you are seeing? > > -hilmar > > On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > >> Hi Hilmar! >> >> Thanks, that's a good thought. But I just tried running it on the >> default 5.8.6 (I have MacOX 10.4), same result: >> >> >> ========================================== >> mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -v >> >> This is perl, v5.8.6 built for darwin-thread-multi-2level >> (with 4 registered patches, see perl -V for more detail) >> >> Copyright 1987-2004, Larry Wall >> >> Perl may be copied only under the terms of either the Artistic License >> or the >> GNU General Public License, which may be found in the Perl 5 source kit. >> >> Complete documentation for Perl, including FAQ lists, should be found on >> this system using `man perl' or `perldoc perl'. If you have access to >> the >> Internet, point your browser at http://www.perl.org/, the Perl Home Page. >> >> >> mws2:~ nick$ perl5.8.6 >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> Can't locate object method "connect" via package "DBI" at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 323. >> ========================================== >> >> >> Just for kicks, I thought it might be a permission issue, so I tried >> it with sudo also, at least I got a different error: >> >> ================== >> mws2:~ nick$ sudo perl5.8.6 >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> Password: >> >> Can't locate DBI.pm in @INC (@INC contains: >> /System/Library/Perl/5.8.6/darwin-thread-multi-2level >> /System/Library/Perl/5.8.6 >> /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 >> /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level >> /Network/Library/Perl/5.8.6 /Network/Library/Perl >> /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level >> /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 195. >> >> BEGIN failed--compilation aborted at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 195. >> ===================== >> >> >> (As for why I installed ActivePerl -- I don't remember, but it seemed >> like a good idea at the time when I was installing various packages >> and something or other requested or suggested the newer version. I >> was a total noob at the time. Still am, sorta...) >> >> Nick >> >> >> Hilmar Lapp wrote: >>> Hi Nick, >>> this is working fine for me, using perl v5.8.8. You may have noticed >>> that DBI does have a method 'connect'. >>> Your perl reports to be 5.10, and to have been built for Mac OSX, yet >>> it is a binary from ActiveState. Is my interpretation correct that >>> you installed this on top of or in place of Mac OSX's native perl >>> v5.8.8? Correspondingly, are you sure that 'perl' (which is what you >>> are calling below), /usr/bin/perl (which is what the script >>> executes), and cpan all are the same perl? >>> If this is all correct and all the right platform, could you try and >>> edit the following code (starting at line 323): >>> my $dbh = DBI->connect($dsn, >>> $user, >>> $pass, >>> { RaiseError => 0, >>> AutoCommit => 1, >>> PrintError => 0, >>> } >>> ) or die $DBI::errstr; >>> by removing the 'or die $DBI::errstr' part. This would be hoping that >>> it's an incompatibility for v5.10. >>> BTW are you sure you need perl 5.10? You will encounter various perl >>> software that has not been tested against it yet (though I think >>> Bioperl has been fixed meanwhile to be compatible). >>> -hilmar >>> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>>> Hi all, >>>> >>>> (sorry that I cross-posted this to the biopython lis, I only just >>>> realized I should get on the bioSQL list) >>>> >>>> >>>> >>>> I'm following the BioSQL tutorial at the biopython website >>>> (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get >>>> bioseqdb to work, and the biosql python scripts etc. >>>> >>>> However I can't get these directions to work in loading the taxonomy >>>> database into bioseqdb. I get: "Can't locate object method >>>> "connect" via package "DBI" " >>>> >>>> I double-checked to make sure I've got DBI in perl (see error >>>> message below) but that doesn't seem to help. >>>> >>>> Any help appreciated! >>>> Nick >>>> >>>> >>>> >>>> commands/returns: >>>> =========================== >>>> mws2:/bioinformatics/eg nick$ perl -v >>>> >>>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>>> (with 3 registered patches, see perl -V for more detail) >>>> >>>> Copyright 1987-2007, Larry Wall >>>> >>>> Binary build 1002 [283697] provided by ActiveState >>>> http://www.ActiveState.com >>>> Built Jan 10 2008 11:08:33 >>>> >>>> Perl may be copied only under the terms of either the Artistic >>>> License or the >>>> GNU General Public License, which may be found in the Perl 5 source >>>> kit. >>>> >>>> Complete documentation for Perl, including FAQ lists, should be >>>> found on >>>> this system using "man perl" or "perldoc perl". If you have access >>>> to the >>>> Internet, point your browser at http://www.perl.org/, the Perl Home >>>> Page. >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>>> Password: >>>> >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /usr/local/Metadata >>>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>>> CPAN: LWP::UserAgent loaded ok (v5.810) >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>>> CPAN: YAML loaded ok (v0.66) >>>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>>> ............................................................................DONE >>>> >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>>> Going to read >>>> /Users/nick/.cpan/sources/modules/02packages.details.txt.gz >>>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>>> ............................................................................DONE >>>> >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>>> ............................................................................DONE >>>> >>>> Going to write /usr/local/Metadata >>>> DBI is up to date (1.607). >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >>>> --dbname bioseqdb --driver mysql --dbuser root --download true >>>> >>>> >>>> Can't locate object method "connect" via package "DBI" at >>>> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >>>> line 323. >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> =========================== >>>> >>>> >>>> >>>> Additional sleuthing: >>>> =========================== >>>> Based on some web advice on this general error I also did this: >>>> >>>> sudo cpan DBD::mysql >>>> >>>> ...which did install something that wasn't installed. But the same >>>> error resulted when the load_ncbi_taxonomy.pl script was run. >>>> =========================== >>>> >>>> >>>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >>>> finding them in @INC or something doesn't seem to be the problem... >>>> >>>> (these commands return '1' if the module is successfully found) >>>> ============ >>>> perl -MDBD::mysql -e 'print 1' >>>> 1 >>>> >>>> perl -MDBI -e 'print 1' >>>> 1 >>>> ============ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> ==================================================== >> Nicholas J. Matzke >> Ph.D. student, Graduate Student Researcher >> Huelsenbeck Lab >> Center for Theoretical Evolutionary Genomics >> 4151 VLSB (Valley Life Sciences Building) >> Department of Integrative Biology >> University of California, Berkeley >> >> Lab websites: >> http://ib.berkeley.edu/people/lab_detail.php?lab=54 >> http://fisher.berkeley.edu/cteg/hlab.html >> Dept. personal page: >> http://ib.berkeley.edu/people/students/person_detail.php?person=370 >> Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html >> Lab phone: 510-643-6299 >> Dept. fax: 510-643-6264 >> Cell phone: 510-301-0179 >> Email: matzke at berkeley.edu >> >> Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology >> VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) >> >> Mailing address: >> Department of Integrative Biology >> 3060 VLSB #3140 >> Berkeley, CA 94720-3140 >> ==================================================== >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From matzke at berkeley.edu Wed Sep 3 18:44:54 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 15:44:54 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BED473.6070006@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> Message-ID: <48BF1366.1020407@berkeley.edu> Well, I'm not sure what I did, but some combination of these things seems to have worked. Your guess is as good as mine... 1. moved the site/lib directory (which contains DBI.pm) to the front of my PERL5LIB (which goes into @INC) export PERL5LIB=$PERL5LIB:/usr/local/ActivePerl-5.10/site/lib:/usr/local/ActivePerl-5.10/man/man3:/usr/local/ActivePerl-5.10/site/lib/Bundle 2. Checked to make sure DBI & DBD::mysql were installed ========================================== mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl -MCPAN -e 'install DBI' CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Mon, 01 Sep 2008 10:02:51 GMT DBI is up to date (1.607). mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl -MCPAN -e 'install DBD::mysql' CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Mon, 01 Sep 2008 10:02:51 GMT DBD::mysql is up to date (4.008). ========================================== 3. (Make sure you have an empty version of the db, at least for me I got errors if I had already loaded sequences etc. into it...I got errors like this: ========================================== note: node (28;331111;27;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (70;300268;69;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (77;3002 ========================================== 4. Ran it again: (I also added '--host localhost') mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true --host localhost Loading NCBI taxon database in taxdata: ... retrieving all taxon nodes in the database ... reading in taxon nodes from nodes.dmp ... insert / update / delete taxon nodes ... (committing nodes) ... rebuilding nested set left/right values ... reading in taxon names from names.dmp ... deleting old taxon names ... inserting new taxon names ... cleaning up Done. So thanks for the help, something or other worked! Cheers, Nick From hlapp at gmx.net Wed Sep 3 18:50:04 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 18:50:04 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BED473.6070006@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> Message-ID: <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote: > [...] > mws2:~ nick$ perldoc -l DBI > > /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm Can you pull up this file in an editor and see what's in there? I think this may just be the CPAN bundle definition (which modules to install together), but not the actual DBI module itself. > > mws2:~ nick$ sudo perldoc -l DBI > Password: > > /usr/local/ActivePerl-5.10/site/lib/DBI.pm If you inspect this one, it will probably be the actual DBI module. So I suspect that your Perl module search paths aren't the same between executing as root or not. If you do 'perl -V' (capital-v) you will see the include path array (@INC) printed at the end. It should be identical whether under sudo or not, but I suspect that for you it will not be the same. If that's indeed the case then the question is why is the path different. As the one for you as normal user is wrong, you can look into your shell initialization files (.tcshrc, .cshrc for csh/ tcsh; .profile, .bash_profile, .login for bash) whether you see anything there that aims to mess with PERL5LIB. Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Sep 3 19:13:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 19:13:48 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF1366.1020407@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> Message-ID: <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> On Sep 3, 2008, at 6:44 PM, Nick Matzke wrote: > Well, I'm not sure what I did, but some combination of these things > seems to have worked. Great we got you going! > [...] > 3. (Make sure you have an empty version of the db, at least for me I > got errors if I had already loaded sequences etc. into it...I got > errors like this: > > ========================================== > note: node (28;331111;27;species;;) is retired; failed to delete: > Cannot delete or update a parent row: a foreign key constraint fails > (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY > (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (70;300268;69;species;;) is retired; failed to delete: > Cannot delete or update a parent row: a foreign key constraint fails > (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY > (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (77;3002 > ========================================== > These aren't fatal, right? What is basically means is that your sequences referenced taxa that are not yet or not anymore in the NCBI taxonomy download. The script doesn't yet process the change log that NCBI also produces. So if two nodes get merged into one, or one gets split into two new, the script can't migrate the data that you already have. Nodes that are in the database but not in the taxonomy dump from NCBI will be considered retired, and the script tries to delete them if there aren't any sequences yet pointing to them. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Wed Sep 3 21:10:16 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 18:10:16 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> Message-ID: <48BF3578.9000806@berkeley.edu> I know my issue is fixed, but just for completeness... Hilmar Lapp wrote: > > On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote: > >> [...] >> mws2:~ nick$ perldoc -l DBI >> >> /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm > > Can you pull up this file in an editor and see what's in there? I think > this may just be the CPAN bundle definition (which modules to install > together), but not the actual DBI module itself. > >> >> mws2:~ nick$ sudo perldoc -l DBI >> Password: >> >> /usr/local/ActivePerl-5.10/site/lib/DBI.pm > > If you inspect this one, it will probably be the actual DBI module. > > So I suspect that your Perl module search paths aren't the same between > executing as root or not. If you do 'perl -V' (capital-v) you will see > the include path array (@INC) printed at the end. It should be identical > whether under sudo or not, but I suspect that for you it will not be the > same. This was indeed true. I couldn't figure out how to fix it though. It appears that sudo doesn't read the .bash_profile file where I have additions to the PERL5LIB environmental variable. Do you know of a way to get sudo to read the standard environmental variables or something like that? Cheers! Thanks again for the help! Nick > If that's indeed the case then the question is why is the path > different. As the one for you as normal user is wrong, you can look into > your shell initialization files (.tcshrc, .cshrc for csh/tcsh; .profile, > .bash_profile, .login for bash) whether you see anything there that aims > to mess with PERL5LIB. > > Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same. > > -hilmar > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From matzke at berkeley.edu Wed Sep 3 21:11:47 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 18:11:47 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> Message-ID: <48BF35D3.9040303@berkeley.edu> Hilmar Lapp wrote: > > On Sep 3, 2008, at 6:44 PM, Nick Matzke wrote: > >> Well, I'm not sure what I did, but some combination of these things >> seems to have worked. > > Great we got you going! > >> [...] >> 3. (Make sure you have an empty version of the db, at least for me I >> got errors if I had already loaded sequences etc. into it...I got >> errors like this: >> >> ========================================== >> note: node (28;331111;27;species;;) is retired; failed to delete: >> Cannot delete or update a parent row: a foreign key constraint fails >> (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY >> (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) >> note: node (70;300268;69;species;;) is retired; failed to delete: >> Cannot delete or update a parent row: a foreign key constraint fails >> (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY >> (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) >> note: node (77;3002 >> ========================================== >> > > These aren't fatal, right? What is basically means is that your > sequences referenced taxa that are not yet or not anymore in the NCBI > taxonomy download. Those weren't fatal, but eventually I hit this and it crashed: ========================================== note: node (4484;312017;4483;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (4490;324602;4489;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) failed to insert node (4577;4577;4575;species;1;1): Duplicate entry '4577' for key 2 at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 581. ========================================== ...but like I said it worked fine on an empty database which was fine for my purposes. Thanks! > > The script doesn't yet process the change log that NCBI also produces. > So if two nodes get merged into one, or one gets split into two new, the > script can't migrate the data that you already have. Nodes that are in > the database but not in the taxonomy dump from NCBI will be considered > retired, and the script tries to delete them if there aren't any > sequences yet pointing to them. > > -hilmar -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From dicknetherlands at gmail.com Mon Sep 1 09:47:01 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Mon, 1 Sep 2008 14:47:01 +0100 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence In-Reply-To: <48BBEF08.8060402@gmx.net> References: <48BBEF08.8060402@gmx.net> Message-ID: You raise two points in this email. The second one, which is easier to deal with, I'll answer first! Bascially yes please do file a bug report about the unique identifiers for features not getting reset on new sequences, using Bugzilla at biojava.org. Now the first one, which relates to your stack trace. Mid way through the stacktrace you see this line: Caused by: java.lang.OutOfMemoryError: Java heap space Basically you're loading loads of stuff into memory and so you're running out of it. Java 5 by default allocates no less than 1/64th and no more than 1/4th of the machine's memory to your program, which you can increase using the -Xms and -Xmx params when starting up your JVM (e.g. when you type the java comand to start your program). Increasing these params will help prevent out of memory messages, particularly if you are dealing with very large sequences. See this link for info on the -Xms and -Xmx options and how they work in various different environments (command line, Tomcat, Eclipse, etc.): http://javahowto.blogspot.com/2006/06/6-common-errors-in-setting-java-heap.html cheers, Richard 2008/9/1 Gabrielle Doan : > Hi Richard, > thanks a lot for your answer. I've changed the size of the rank in the > BioSQL table seqfeature from smallint unsigned to int unsigned. So that the > error messages because of the rank do not occur anymore. > But now I'm facing an other problem. If I try to insert a new feature to > human chromosome 1 and 2 into my database I get following message: > > org.hibernate.PropertyAccessException: Exception occurred inside getter of > org.biojavax.bio.seq.SimpleRichSequence.stringSequence > at > org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:148) > at > org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:256) > at > org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:209) > at > org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:3581) > at > org.hibernate.event.def.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:167) > at > org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:120) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:196) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:76) > at > org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) > at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) > at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) > at > org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) > at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) > at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) > at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:145) > ... 14 more > Caused by: java.lang.OutOfMemoryError: Java heap space > at java.util.Arrays.copyOf(Arrays.java:2882) > at > java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100) > at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:572) > at java.lang.StringBuffer.append(StringBuffer.java:320) > at > org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTokenization.java:214) > at > org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenizeSymbolList(AlphabetManager.java:1460) > at > org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:102) > at > org.biojavax.bio.seq.DummyRichSequenceHandler.seqString(DummyRichSequenceHandler.java:115) > at > org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.seqString(BioSQLRichSequenceHandler.java:155) > at > org.biojavax.bio.seq.ThinRichSequence.seqString(ThinRichSequence.java:188) > at > org.biojavax.bio.seq.SimpleRichSequence.getStringSequence(SimpleRichSequence.java:77) > ... 19 more > > I also had a conversation with Hilmar Lapp, who told me that there's > possibly a bug in BioJava because the unique property does hold for the four > elements bioentry_id, type_term_id, source_term_id and rank but it seems > that BioJava always inkrements the rank for each new feature. Should I post > a bug report? > > It would be very nice if you could help me. I am grateful for any > hints. Thanks a lot. > > cheers > Gabrielle > > > > > > -------- Original-Nachricht -------- > Betreff: Re: [Biojava-l] Problems with adding miRNA to sequence > Datum: Thu, 28 Aug 2008 23:45:35 +0100 > Von: Richard Holland > An: Gabrielle Doan > CC: biojava-l at biojava.org > Referenzen: <48B6B354.6010307 at gmx.net> > > Looks like your sequence has so many features that it exceeds the > maximum permitted by BioSQL: > > com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of > range value adjusted for column 'rank' at row 1 > > Not sure what you can do about this other than go to the Feature table > in your database and increase the maximum value allowed in the 'rank' > column. > > cheers, > Richard > > > 2008/8/28 Gabrielle Doan : >> >> Hi all, >> I would like to insert new features (miRNA) into my exitsting BioSQL >> database. At the moment the database contains the chromosomes 1-22, X, Y >> and MT downloaded from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/. And >> now I have tried to add the information about miRNA from >> http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl into my >> database with following code: >> >> private void makeAFeature(String id, String chr, int startpos, >> int endpos, Strand strand, float score, String gene) >> throws ChangeVetoExceptionIllegalSymbolException >> { >> RichSequence rs = chromosomes.get(chr); >> if (rs == null) { >> rs = db.SearchForSequence(chr); >> chromosomes.put(chr, rs); >> } >> RichFeature feat = RichFeature.Tools.makeEmptyFeature(); >> feat.setName(id); >> RichLocation rl = new SimpleRichLocation(new >> >> SimplePosition(startpos),new SimplePosition(endpos), >> 1,strand); >> feat.setLocation(rl); >> try { >> >> feat.setTypeTerm(RichObjectFactory.getDefaultOntology() >> .getOrCreateTerm("miRNA")); >> feat.setType(feat.getTypeTerm().getName()); >> } catch (InvalidTermException e) { >> // TODO Auto-generated catch block >> e.printStackTrace(); >> } >> feat.getAnnotation().setProperty("score", >> Float.valueOf(score)); >> feat.getAnnotation().setProperty("gene", gene); >> feat.setParent(rs); >> rs.getFeatureSet().add(feat); >> } >> >> I successfully inserted the information for chromosome 3-22, X, Y and MT. >> But when I try to deal with chromosome 1, 2 in the same way I get >> following message: >> >> org.hibernate.exception.DataException: could not insert: [Feature] >> at >> >> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) >> at >> >> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) >> at >> >> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40) >> at >> >> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163) >> at >> >> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643) >> at >> >> org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51) >> at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) >> at >> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507) >> at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) >> at >> org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218) >> at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268) >> at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) >> at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) >> at >> org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296) >> at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242) >> at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) >> at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) >> at org.hibernate.engine.Cascade.cascade(Cascade.java:130) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65) >> at >> >> org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) >> at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) >> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) >> at >> org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) >> at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) >> at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) >> at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) >> Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of >> range value adjusted for column 'rank' at row 1 >> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973) >> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) >> at >> >> com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129) >> at >> >> com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268) >> at >> >> org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73) >> at >> >> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33) >> ... 32 more >> >> It would be very nice if someone could help me. I am grateful for any >> hints. Thanks a lot. >> >> Cheers, >> Gabrielle >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -- > Richard Holland > Finance Director > Eagle Genomics > http://www.eaglegenomics.com/ > > -- Richard Holland Finance Director Eagle Genomics http://www.eaglegenomics.com/ From hlapp at gmx.net Thu Sep 4 10:07:44 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:07:44 -0400 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence In-Reply-To: References: <48BBEF08.8060402@gmx.net> Message-ID: On Sep 1, 2008, at 9:47 AM, Richard Holland wrote: > Bascially yes please do file a bug report about the unique > identifiers for features not getting reset on new sequences Just for clarification, the bug appears to be not to reset the rank for every new combination of feature type and source terms, for the same sequence. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Sep 4 10:25:16 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:25:16 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF3578.9000806@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> <48BF3578.9000806@berkeley.edu> Message-ID: On Sep 3, 2008, at 9:10 PM, Nick Matzke wrote: > Do you know of a way to get sudo to read the standard environmental > variables or something like that? You can put them in the shell initialization files of the target user (root in your examples). Note that sudo will remove the PERL5LIB, PERLLIB, and PERLOPT environment variables when invoked, so as it turns out that invoking perl w/ and w/o sudo isn't the same is actually by design if you have have PERL5LIB changed for your local user. In reality there should rarely if ever be a need to use sudo when running a biosql, bioperl-db, or bioperl perl script. Are you sure you need to do this? The reason you saw the problems were most likely because the directory //Bundle was in PERL5LIB, and was so relatively at the front. I doubt that it needs to be there to begin with; have you observed any failures or problems if you remove that directory completely? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Sep 4 10:28:37 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:28:37 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF35D3.9040303@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> <48BF35D3.9040303@berkeley.edu> Message-ID: <46C49E37-B9F1-4009-9E16-A976582908ED@gmx.net> On Sep 3, 2008, at 9:11 PM, Nick Matzke wrote: > Those weren't fatal, but eventually I hit this and it crashed: > > ========================================== > note: node (4484;312017;4483;species;;) is retired; failed to > delete: Cannot delete or update a parent row: a foreign key > constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` > FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (4490;324602;4489;species;;) is retired; failed to > delete: Cannot delete or update a parent row: a foreign key > constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` > FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > failed to insert node (4577;4577;4575;species;1;1): Duplicate entry > '4577' for key 2 at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 581. > ========================================== > > ...but like I said it worked fine on an empty database which was > fine for my purposes. I think this might be fixed in BioSQL v1.0.1. (v1.0.1 fixes the load_ncbi_taxonomy.pl script to no longer assume or require the primary key and the NCBI taxonID be identical, which I think is the reason the failing insert above was an insert rather than the update it should have been). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From tatedger at googlemail.com Thu Sep 25 11:23:46 2008 From: tatedger at googlemail.com (john paul) Date: Thu, 25 Sep 2008 16:23:46 +0100 Subject: [BioSQL-l] Can't locate object method "get_dbxrefs" Message-ID: Hello guys, I need to pick your brain on this. I was trying to load some sequences in a fresh RH build using bioperl-db and got the following error: [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost --dbuser root --dbname biosql --namespace swissprot --format swiss /home/tatedger/tmp/uniprot_sprot.dat --testonly Loading /home/tatedger/tmp/uniprot_sprot.dat ... Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line 552, line 70. I have seen some posts on this regard ( http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but it wasn't clear to me what the solution would be. My configuration: - mysql version 4.1.7 - Red Hat Enterprise Linux ES release 4 (Nahant) to install bioperl and bioperl-db I used the help found on the website following - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. bioperl-db test 04 shows the same error. [tatedger at localhost bioperl-db]$ perl t/04swiss.t 1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line 552, line 78. my @INC file looks like /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl What am I doing wrong? Could you help? Thanks in advance for your help Tom From tatedger at googlemail.com Thu Sep 25 12:27:29 2008 From: tatedger at googlemail.com (john paul) Date: Thu, 25 Sep 2008 17:27:29 +0100 Subject: [BioSQL-l] [Bioperl-l] Can't locate object method "get_dbxrefs" In-Reply-To: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> References: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> Message-ID: On Thu, Sep 25, 2008 at 4:40 PM, Brian Osborne wrote: > John, > > What does: > > >locate Bio/Ontology/Term.pm > > Say? > Silly me. $ locate Bio/Ontology/Term.pm /usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm and $ cat /usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm|grep get_dbxrefs produced no answer the latest version posted by Sendu on cpan says for that module # $Id: Term.pm,v 1.31.4.1 2006/10/02 23:10:22 sendu Exp $ # # BioPerl module for Bio::Ontology::Term and the live version at ( http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/Ontology/Term.pm ) says # $Id: Term.pm 14708 2008-06-10 00:08:17Z heikki $ # # BioPerl module for Bio::Ontology::Term # I was using an old distribution from CPAN. reinstalling from the main trunk svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live solved the problem. Thanks again Tom > > Brian O. > > > > On Sep 25, 2008, at 11:23 AM, john paul wrote: > > Hello guys, >> >> I need to pick your brain on this. I was trying to load some sequences in >> a >> fresh RH build using bioperl-db and got the following error: >> >> [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost >> --dbuser root --dbname biosql --namespace swissprot --format swiss >> /home/tatedger/tmp/uniprot_sprot.dat --testonly >> Loading /home/tatedger/tmp/uniprot_sprot.dat ... >> Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via >> package >> "Bio::Ontology::Term" at >> /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line >> 552, line 70. >> >> >> I have seen some posts on this regard ( >> http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but it >> wasn't >> clear to me what the solution would be. >> >> >> My configuration: >> - mysql version 4.1.7 >> - Red Hat Enterprise Linux ES release 4 (Nahant) >> >> to install bioperl and bioperl-db I used the help found on the website >> following >> - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz >> - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db >> - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. >> >> bioperl-db test 04 shows the same error. >> >> [tatedger at localhost bioperl-db]$ perl t/04swiss.t >> 1..52 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" >> at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm >> line >> 552, line 78. >> >> >> my @INC file looks like >> /usr/lib/perl5/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/5.8.5 >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.5 >> /usr/lib/perl5/site_perl/5.8.4 >> /usr/lib/perl5/site_perl/5.8.3 >> /usr/lib/perl5/site_perl/5.8.2 >> /usr/lib/perl5/site_perl/5.8.1 >> /usr/lib/perl5/site_perl/5.8.0 >> /usr/lib/perl5/site_perl >> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.5 >> /usr/lib/perl5/vendor_perl/5.8.4 >> /usr/lib/perl5/vendor_perl/5.8.3 >> /usr/lib/perl5/vendor_perl/5.8.2 >> /usr/lib/perl5/vendor_perl/5.8.1 >> /usr/lib/perl5/vendor_perl/5.8.0 >> /usr/lib/perl5/vendor_perl >> >> What am I doing wrong? Could you help? >> >> Thanks in advance for your help >> Tom >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From biopython at maubp.freeserve.co.uk Fri Sep 26 09:56:24 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 26 Sep 2008 14:56:24 +0100 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? Message-ID: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Hi All, In BioSQL v1.0.1, fields bioentry.accession and dbxref.accession were increased from 40 to 128 characters. See http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html However, bioentry.name and bioentry.identifier are still only 40 characters - which seems a bit short, given that BioPerl's load_seqdatabase.pl seems to put the full contents of a FASTA identifier (up to the first space) in both bioentry.name and bioentry.identifier fields. I've just been dealing with Biopython and loading FASTA files into BioSQL (Bug 2425) and a similar concern applies here. Has anyone had any real world problems with the bioentry.name and bioentry.identifier fields being too small? Peter From hlapp at gmx.net Fri Sep 26 10:24:57 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 26 Sep 2008 10:24:57 -0400 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Message-ID: Interesting. I see your logic and I guess you have a point. I've almost exclusively been loading all kinds of genbank, {swiss,uni}prot, unigene etc files, which don't suffer from this problem, as the name then is either identical to the accession, or is a short gene symbol, and the identifier is the GI#, or empty. I myself wouldn't load FASTA files w/o any processing/parsing the identifier token, but maybe that's not a reasonable expectation to put on everyone else? -hilmar On Sep 26, 2008, at 9:56 AM, Peter wrote: > Hi All, > > In BioSQL v1.0.1, fields bioentry.accession and dbxref.accession were > increased from 40 to 128 characters. See > http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html > > However, bioentry.name and bioentry.identifier are still only 40 > characters - which seems a bit short, given that BioPerl's > load_seqdatabase.pl seems to put the full contents of a FASTA > identifier (up to the first space) in both bioentry.name and > bioentry.identifier fields. I've just been dealing with Biopython and > loading FASTA files into BioSQL (Bug 2425) and a similar concern > applies here. > > Has anyone had any real world problems with the bioentry.name and > bioentry.identifier fields being too small? > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Fri Sep 26 10:46:19 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 26 Sep 2008 15:46:19 +0100 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Message-ID: <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> On Fri, Sep 26, 2008 at 3:24 PM, Hilmar Lapp wrote: > > Interesting. I see your logic and I guess you have a point. > > I've almost exclusively been loading all kinds of genbank, {swiss,uni}prot, > unigene etc files, which don't suffer from this problem, as the name then is > either identical to the accession, or is a short gene symbol, and the > identifier is the GI#, or empty. In my case its also been mostly GenBank files, where long names are not an issue. > I myself wouldn't load FASTA files w/o any processing/parsing the identifier > token, but maybe that's not a reasonable expectation to put on everyone > else? I think is not unreasonable to want to import FASTA files directly (but this is not something I've actually done other than for testing). For example, I might want to import NCBI FASTA files directly, but these probably have names under 40 letters. Another example would be sequencing or assembly output, but I don't have a feel for what kind of length names are used here. I was half expecting someone on the list to say "Oh yes - we had to increase the field size when we were importing XYZ". Peter From barry.moore at genetics.utah.edu Fri Sep 26 11:00:51 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 26 Sep 2008 09:00:51 -0600 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> Message-ID: I've tweaked some of those varchars in the past on local installations, but I can't remember off the top of my head if I did that for name - probably not. I would to agree with the emerging view though - I don't know that I would need longer names right now, but it hardly makes sense to have an accession length of 128 and a name length of 40 since the name may well be or include the accession. B Barry Moore Senior Research Specialist Eccles Institute of Human Genetics Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 On Sep 26, 2008, at 8:46 AM, Peter wrote: > On Fri, Sep 26, 2008 at 3:24 PM, Hilmar Lapp wrote: >> >> Interesting. I see your logic and I guess you have a point. >> >> I've almost exclusively been loading all kinds of genbank, >> {swiss,uni}prot, >> unigene etc files, which don't suffer from this problem, as the >> name then is >> either identical to the accession, or is a short gene symbol, and the >> identifier is the GI#, or empty. > > In my case its also been mostly GenBank files, where long names are > not an issue. > >> I myself wouldn't load FASTA files w/o any processing/parsing the >> identifier >> token, but maybe that's not a reasonable expectation to put on >> everyone >> else? > > I think is not unreasonable to want to import FASTA files directly > (but this > is not something I've actually done other than for testing). For > example, > I might want to import NCBI FASTA files directly, but these > probably have > names under 40 letters. Another example would be sequencing or > assembly > output, but I don't have a feel for what kind of length names are > used here. > > I was half expecting someone on the list to say "Oh yes - we had to > increase > the field size when we were importing XYZ". > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From bosborne11 at verizon.net Thu Sep 25 11:40:45 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 25 Sep 2008 11:40:45 -0400 Subject: [BioSQL-l] [Bioperl-l] Can't locate object method "get_dbxrefs" In-Reply-To: References: Message-ID: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> John, What does: >locate Bio/Ontology/Term.pm Say? Brian O. On Sep 25, 2008, at 11:23 AM, john paul wrote: > Hello guys, > > I need to pick your brain on this. I was trying to load some > sequences in a > fresh RH build using bioperl-db and got the following error: > > [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost > --dbuser root --dbname biosql --namespace swissprot --format swiss > /home/tatedger/tmp/uniprot_sprot.dat --testonly > Loading /home/tatedger/tmp/uniprot_sprot.dat ... > Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via > package > "Bio::Ontology::Term" at > /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm > line > 552, line 70. > > > I have seen some posts on this regard ( > http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but > it wasn't > clear to me what the solution would be. > > > My configuration: > - mysql version 4.1.7 > - Red Hat Enterprise Linux ES release 4 (Nahant) > > to install bioperl and bioperl-db I used the help found on the website > following > - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz > - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db > - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. > > bioperl-db test 04 shows the same error. > > [tatedger at localhost bioperl-db]$ perl t/04swiss.t > 1..52 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > Can't locate object method "get_dbxrefs" via package > "Bio::Ontology::Term" > at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/ > PersistentObject.pm line > 552, line 78. > > > my @INC file looks like > /usr/lib/perl5/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/5.8.5 > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.5 > /usr/lib/perl5/site_perl/5.8.4 > /usr/lib/perl5/site_perl/5.8.3 > /usr/lib/perl5/site_perl/5.8.2 > /usr/lib/perl5/site_perl/5.8.1 > /usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.5 > /usr/lib/perl5/vendor_perl/5.8.4 > /usr/lib/perl5/vendor_perl/5.8.3 > /usr/lib/perl5/vendor_perl/5.8.2 > /usr/lib/perl5/vendor_perl/5.8.1 > /usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl > > What am I doing wrong? Could you help? > > Thanks in advance for your help > Tom > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From gabrielle_doan at gmx.net Mon Sep 1 13:32:56 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Mon, 01 Sep 2008 15:32:56 +0200 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence Message-ID: <48BBEF08.8060402@gmx.net> Hi Richard, thanks a lot for your answer. I've changed the size of the rank in the BioSQL table seqfeature from smallint unsigned to int unsigned. So that the error messages because of the rank do not occur anymore. But now I'm facing an other problem. If I try to insert a new feature to human chromosome 1 and 2 into my database I get following message: org.hibernate.PropertyAccessException: Exception occurred inside getter of org.biojavax.bio.seq.SimpleRichSequence.stringSequence at org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:148) at org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:256) at org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:209) at org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:3581) at org.hibernate.event.def.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:167) at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:120) at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:196) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:76) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:145) ... 14 more Caused by: java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:2882) at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100) at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:572) at java.lang.StringBuffer.append(StringBuffer.java:320) at org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTokenization.java:214) at org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenizeSymbolList(AlphabetManager.java:1460) at org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:102) at org.biojavax.bio.seq.DummyRichSequenceHandler.seqString(DummyRichSequenceHandler.java:115) at org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.seqString(BioSQLRichSequenceHandler.java:155) at org.biojavax.bio.seq.ThinRichSequence.seqString(ThinRichSequence.java:188) at org.biojavax.bio.seq.SimpleRichSequence.getStringSequence(SimpleRichSequence.java:77) ... 19 more I also had a conversation with Hilmar Lapp, who told me that there's possibly a bug in BioJava because the unique property does hold for the four elements bioentry_id, type_term_id, source_term_id and rank but it seems that BioJava always inkrements the rank for each new feature. Should I post a bug report? It would be very nice if you could help me. I am grateful for any hints. Thanks a lot. cheers Gabrielle -------- Original-Nachricht -------- Betreff: Re: [Biojava-l] Problems with adding miRNA to sequence Datum: Thu, 28 Aug 2008 23:45:35 +0100 Von: Richard Holland An: Gabrielle Doan CC: biojava-l at biojava.org Referenzen: <48B6B354.6010307 at gmx.net> Looks like your sequence has so many features that it exceeds the maximum permitted by BioSQL: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of range value adjusted for column 'rank' at row 1 Not sure what you can do about this other than go to the Feature table in your database and increase the maximum value allowed in the 'rank' column. cheers, Richard 2008/8/28 Gabrielle Doan : > > Hi all, > I would like to insert new features (miRNA) into my exitsting BioSQL > database. At the moment the database contains the chromosomes 1-22, X, Y > and MT downloaded from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/. And > now I have tried to add the information about miRNA from > http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl into my > database with following code: > > private void makeAFeature(String id, String chr, int startpos, > int endpos, Strand strand, float score, String gene) > throws ChangeVetoExceptionIllegalSymbolException > { > RichSequence rs = chromosomes.get(chr); > if (rs == null) { > rs = db.SearchForSequence(chr); > chromosomes.put(chr, rs); > } > RichFeature feat = RichFeature.Tools.makeEmptyFeature(); > feat.setName(id); > RichLocation rl = new SimpleRichLocation(new > > SimplePosition(startpos),new SimplePosition(endpos), > 1,strand); > feat.setLocation(rl); > try { > > feat.setTypeTerm(RichObjectFactory.getDefaultOntology() > .getOrCreateTerm("miRNA")); > feat.setType(feat.getTypeTerm().getName()); > } catch (InvalidTermException e) { > // TODO Auto-generated catch block > e.printStackTrace(); > } > feat.getAnnotation().setProperty("score", > Float.valueOf(score)); > feat.getAnnotation().setProperty("gene", gene); > feat.setParent(rs); > rs.getFeatureSet().add(feat); > } > > I successfully inserted the information for chromosome 3-22, X, Y and MT. > But when I try to deal with chromosome 1, 2 in the same way I get > following message: > > org.hibernate.exception.DataException: could not insert: [Feature] > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643) > at > org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51) > at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) > at > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298) > at > org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181) > at > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) > at > org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507) > at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) > at > org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218) > at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268) > at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) > at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) > at > org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296) > at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242) > at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) > at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) > at org.hibernate.engine.Cascade.cascade(Cascade.java:130) > at > org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131) > at > org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65) > at > org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) > at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) > at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) > at > org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) > at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) > at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) > at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) > Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of > range value adjusted for column 'rank' at row 1 > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at > com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129) > at > com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268) > at > org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33) > ... 32 more > > It would be very nice if someone could help me. I am grateful for any > hints. Thanks a lot. > > Cheers, > Gabrielle > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland Finance Director Eagle Genomics http://www.eaglegenomics.com/ From gabrielle_doan at gmx.net Mon Sep 1 13:38:28 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Mon, 01 Sep 2008 15:38:28 +0200 Subject: [BioSQL-l] [Fwd: Re: Increasing value of rank in table seqfeature] Message-ID: <48BBF054.50900@gmx.net> Hi Hilmar, you are right. I'm using BioJava to insert the features into my database. I'm suprised at the rank because in my source code I always set the rank to zero for each new feature I want to add to the human chromosome 1 and 2. But in my database the rank is always incremented. private void makeAFeature(String id, String chr, int startpos, int endpos, Strand strand, float score, String gene) throws ChangeVetoException, IllegalSymbolException { RichSequence rs = chromosomes.get(chr); if (rs == null) { rs = db.SearchForSequence(chr); chromosomes.put(chr, rs); } RichFeature feat = RichFeature.Tools.makeEmptyFeature(); // System.out.println("setParent " + rs.getName()); feat.setName(id); RichLocation rl = new SimpleRichLocation(new SimplePosition(startpos),new SimplePosition(endpos), 0, strand); feat.setLocation(rl); try { feat.setTypeTerm(RichObjectFactory.getDefaultOntology() .getOrCreateTerm("miRNA")); feat.setType(feat.getTypeTerm().getName()); } catch (InvalidTermException e) { // TODO Auto-generated catch block e.printStackTrace(); } feat.getAnnotation().setProperty("score", Float.valueOf(score)); feat.getAnnotation().setProperty("gene", gene); feat.setParent(rs); rs.getFeatureSet().add(feat); } It would be very nice if you could help me or give me any hint. Thanks a lot. cheers, Gabrielle -------- Original-Nachricht -------- Betreff: Re: [BioSQL-l] Increasing value of rank in table seqfeature Datum: Fri, 29 Aug 2008 10:45:26 -0400 Von: Hilmar Lapp An: Gabrielle Doan CC: biosql-l at lists.open-bio.org Referenzen: <48B7ED4A.5000008 at gmx.net> Hi Gabrielle, smallint can take values up to 65535 if unsigned. I can see that this can become a limitation if the bioentry to which the features belong is a whole chromosome. Note that the uniqueness constraint is not on bioentry (sequence) and rank. Instead, it is on the combination of bioentry (sequence), type term, source term, and rank. I.e., at present, with the smallint constraint, you can't have more than 65535 features of the same type and from the same source for a particular sequence. It's possible that the software you are using (Biojava?) increments the rank for every single feature, rather than resetting for each new combination of type and source. Is that what you are seeing? -hilmar On Aug 29, 2008, at 8:36 AM, Gabrielle Doan wrote: > Hi all, > I have a BioSQL database which contains several chromosomes and > features. And now I would like to insert chromosome 2 with some > miRNA as a new feature. I meet the problem that in the table > seqfeature the entry rank just can store smallint(5) unsigned > values. As fare as I know each rank has to be unique. If you want to > store many information this value will be excess quickly. Isn't it > better to increase this value? > > It would be very nice if someone could comment my suggestion. Thanks > a lot. > > Cheers, > Gabrielle > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Tue Sep 2 23:52:18 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Tue, 02 Sep 2008 16:52:18 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb Message-ID: <48BDD1B2.80407@berkeley.edu> Hi all, (sorry that I cross-posted this to the biopython lis, I only just realized I should get on the bioSQL list) I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get bioseqdb to work, and the biosql python scripts etc. However I can't get these directions to work in loading the taxonomy database into bioseqdb. I get: "Can't locate object method "connect" via package "DBI" " I double-checked to make sure I've got DBI in perl (see error message below) but that doesn't seem to help. Any help appreciated! Nick commands/returns: =========================== mws2:/bioinformatics/eg nick$ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 3 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com Built Jan 10 2008 11:08:33 Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page. mws2:/bioinformatics/eg nick$ sudo cpan DBI Password: CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Wed, 23 Jul 2008 10:02:50 GMT CPAN: LWP::UserAgent loaded ok (v5.810) CPAN: Time::HiRes loaded ok (v1.9711) Fetching with LWP: http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz CPAN: YAML loaded ok (v0.66) Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz ............................................................................DONE Fetching with LWP: http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz Database was generated on Mon, 01 Sep 2008 10:02:51 GMT ............................................................................DONE Fetching with LWP: http://ppm.activestate.com/CPAN/modules/03modlist.data.gz Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz ............................................................................DONE Going to write /usr/local/Metadata DBI is up to date (1.607). mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Can't locate object method "connect" via package "DBI" at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 323. mws2:/bioinformatics/eg nick$ =========================== Additional sleuthing: =========================== Based on some web advice on this general error I also did this: sudo cpan DBD::mysql ...which did install something that wasn't installed. But the same error resulted when the load_ncbi_taxonomy.pl script was run. =========================== Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not finding them in @INC or something doesn't seem to be the problem... (these commands return '1' if the module is successfully found) ============ perl -MDBD::mysql -e 'print 1' 1 perl -MDBI -e 'print 1' 1 ============ From hlapp at gmx.net Wed Sep 3 03:31:36 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 2 Sep 2008 23:31:36 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BDD1B2.80407@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> Message-ID: Hi Nick, this is working fine for me, using perl v5.8.8. You may have noticed that DBI does have a method 'connect'. Your perl reports to be 5.10, and to have been built for Mac OSX, yet it is a binary from ActiveState. Is my interpretation correct that you installed this on top of or in place of Mac OSX's native perl v5.8.8? Correspondingly, are you sure that 'perl' (which is what you are calling below), /usr/bin/perl (which is what the script executes), and cpan all are the same perl? If this is all correct and all the right platform, could you try and edit the following code (starting at line 323): my $dbh = DBI->connect($dsn, $user, $pass, { RaiseError => 0, AutoCommit => 1, PrintError => 0, } ) or die $DBI::errstr; by removing the 'or die $DBI::errstr' part. This would be hoping that it's an incompatibility for v5.10. BTW are you sure you need perl 5.10? You will encounter various perl software that has not been tested against it yet (though I think Bioperl has been fixed meanwhile to be compatible). -hilmar On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: > Hi all, > > (sorry that I cross-posted this to the biopython lis, I only just > realized I should get on the bioSQL list) > > > > I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy > ). I can get bioseqdb to work, and the biosql python scripts etc. > > However I can't get these directions to work in loading the taxonomy > database into bioseqdb. I get: "Can't locate object method > "connect" via package "DBI" " > > I double-checked to make sure I've got DBI in perl (see error > message below) but that doesn't seem to help. > > Any help appreciated! > Nick > > > > commands/returns: > =========================== > mws2:/bioinformatics/eg nick$ perl -v > > This is perl, v5.10.0 built for darwin-thread-multi-2level > (with 3 registered patches, see perl -V for more detail) > > Copyright 1987-2007, Larry Wall > > Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com > Built Jan 10 2008 11:08:33 > > Perl may be copied only under the terms of either the Artistic > License or the > GNU General Public License, which may be found in the Perl 5 source > kit. > > Complete documentation for Perl, including FAQ lists, should be > found on > this system using "man perl" or "perldoc perl". If you have access > to the > Internet, point your browser at http://www.perl.org/, the Perl Home > Page. > > > > > > > mws2:/bioinformatics/eg nick$ sudo cpan DBI > Password: > > CPAN: Storable loaded ok (v2.18) > Going to read /usr/local/Metadata > Database was generated on Wed, 23 Jul 2008 10:02:50 GMT > CPAN: LWP::UserAgent loaded ok (v5.810) > CPAN: Time::HiRes loaded ok (v1.9711) > Fetching with LWP: > http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz > CPAN: YAML loaded ok (v0.66) > Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz > ............................................................................DONE > Fetching with LWP: > http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz > Going to read /Users/nick/.cpan/sources/modules/ > 02packages.details.txt.gz > Database was generated on Mon, 01 Sep 2008 10:02:51 GMT > ............................................................................DONE > Fetching with LWP: > http://ppm.activestate.com/CPAN/modules/03modlist.data.gz > Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz > ............................................................................DONE > Going to write /usr/local/Metadata > DBI is up to date (1.607). > > > > > > > mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ > biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- > driver mysql --dbuser root --download true > > > Can't locate object method "connect" via package "DBI" at / > bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 323. > > mws2:/bioinformatics/eg nick$ > =========================== > > > > Additional sleuthing: > =========================== > Based on some web advice on this general error I also did this: > > sudo cpan DBD::mysql > > ...which did install something that wasn't installed. But the same > error resulted when the load_ncbi_taxonomy.pl script was run. > =========================== > > > Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not > finding them in @INC or something doesn't seem to be the problem... > > (these commands return '1' if the module is successfully found) > ============ > perl -MDBD::mysql -e 'print 1' > 1 > > perl -MDBI -e 'print 1' > 1 > ============ > > > > > > > > > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Wed Sep 3 03:57:02 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Tue, 02 Sep 2008 20:57:02 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: References: <48BDD1B2.80407@berkeley.edu> Message-ID: <48BE0B0E.6040604@berkeley.edu> Hi Hilmar! Thanks, that's a good thought. But I just tried running it on the default 5.8.6 (I have MacOX 10.4), same result: ========================================== mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' 1 mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' 1 mws2:~ nick$ perl5.8.6 -v This is perl, v5.8.6 built for darwin-thread-multi-2level (with 4 registered patches, see perl -V for more detail) Copyright 1987-2004, Larry Wall Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using `man perl' or `perldoc perl'. If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page. mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Can't locate object method "connect" via package "DBI" at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 323. ========================================== Just for kicks, I thought it might be a permission issue, so I tried it with sudo also, at least I got a different error: ================== mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true Password: Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. ===================== (As for why I installed ActivePerl -- I don't remember, but it seemed like a good idea at the time when I was installing various packages and something or other requested or suggested the newer version. I was a total noob at the time. Still am, sorta...) Nick Hilmar Lapp wrote: > Hi Nick, > > this is working fine for me, using perl v5.8.8. You may have noticed > that DBI does have a method 'connect'. > > Your perl reports to be 5.10, and to have been built for Mac OSX, yet it > is a binary from ActiveState. Is my interpretation correct that you > installed this on top of or in place of Mac OSX's native perl v5.8.8? > Correspondingly, are you sure that 'perl' (which is what you are calling > below), /usr/bin/perl (which is what the script executes), and cpan all > are the same perl? > > If this is all correct and all the right platform, could you try and > edit the following code (starting at line 323): > > my $dbh = DBI->connect($dsn, > $user, > $pass, > { RaiseError => 0, > AutoCommit => 1, > PrintError => 0, > } > ) or die $DBI::errstr; > > by removing the 'or die $DBI::errstr' part. This would be hoping that > it's an incompatibility for v5.10. > > BTW are you sure you need perl 5.10? You will encounter various perl > software that has not been tested against it yet (though I think Bioperl > has been fixed meanwhile to be compatible). > > -hilmar > > On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: > >> Hi all, >> >> (sorry that I cross-posted this to the biopython lis, I only just >> realized I should get on the bioSQL list) >> >> >> >> I'm following the BioSQL tutorial at the biopython website >> (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get >> bioseqdb to work, and the biosql python scripts etc. >> >> However I can't get these directions to work in loading the taxonomy >> database into bioseqdb. I get: "Can't locate object method "connect" >> via package "DBI" " >> >> I double-checked to make sure I've got DBI in perl (see error message >> below) but that doesn't seem to help. >> >> Any help appreciated! >> Nick >> >> >> >> commands/returns: >> =========================== >> mws2:/bioinformatics/eg nick$ perl -v >> >> This is perl, v5.10.0 built for darwin-thread-multi-2level >> (with 3 registered patches, see perl -V for more detail) >> >> Copyright 1987-2007, Larry Wall >> >> Binary build 1002 [283697] provided by ActiveState >> http://www.ActiveState.com >> Built Jan 10 2008 11:08:33 >> >> Perl may be copied only under the terms of either the Artistic License >> or the >> GNU General Public License, which may be found in the Perl 5 source kit. >> >> Complete documentation for Perl, including FAQ lists, should be found on >> this system using "man perl" or "perldoc perl". If you have access to >> the >> Internet, point your browser at http://www.perl.org/, the Perl Home Page. >> >> >> >> >> >> >> mws2:/bioinformatics/eg nick$ sudo cpan DBI >> Password: >> >> CPAN: Storable loaded ok (v2.18) >> Going to read /usr/local/Metadata >> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >> CPAN: LWP::UserAgent loaded ok (v5.810) >> CPAN: Time::HiRes loaded ok (v1.9711) >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >> CPAN: YAML loaded ok (v0.66) >> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >> ............................................................................DONE >> >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >> Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz >> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >> ............................................................................DONE >> >> Fetching with LWP: >> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >> ............................................................................DONE >> >> Going to write /usr/local/Metadata >> DBI is up to date (1.607). >> >> >> >> >> >> >> mws2:/bioinformatics/eg nick$ >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> >> Can't locate object method "connect" via package "DBI" at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 323. >> >> mws2:/bioinformatics/eg nick$ >> =========================== >> >> >> >> Additional sleuthing: >> =========================== >> Based on some web advice on this general error I also did this: >> >> sudo cpan DBD::mysql >> >> ...which did install something that wasn't installed. But the same >> error resulted when the load_ncbi_taxonomy.pl script was run. >> =========================== >> >> >> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >> finding them in @INC or something doesn't seem to be the problem... >> >> (these commands return '1' if the module is successfully found) >> ============ >> perl -MDBD::mysql -e 'print 1' >> 1 >> >> perl -MDBI -e 'print 1' >> 1 >> ============ >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From hlapp at gmx.net Wed Sep 3 15:43:49 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 11:43:49 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BE0B0E.6040604@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> Message-ID: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Hi Nick, this is pretty weird. But the two different results between running with and without sudo strongly indicate that something's wrong with your perl installation setup. Specifically, DBI apparently isn't installed, and the DBI module that you are picking up without the sudo seems to be wrong or a corrupt one. You can ask perldoc for the full path to the module using the -l argument: $ perldoc -l DBI $ sudo perldoc -l DBI $ /usr/bin/perldoc -l DBI $ sudo /usr/bin/perldoc -l DBI should all yield the same result, and the following should, too: $ perl -e 'use DBI; $dbh=DBI- >connect("dbi:mysql:database=test","","");' w/ and w/o using the full path, w/ and w/o prepending sudo. Is that what you are seeing? -hilmar On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > Hi Hilmar! > > Thanks, that's a good thought. But I just tried running it on the > default 5.8.6 (I have MacOX 10.4), same result: > > > ========================================== > mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' > 1 > > mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' > 1 > > mws2:~ nick$ perl5.8.6 -v > > This is perl, v5.8.6 built for darwin-thread-multi-2level > (with 4 registered patches, see perl -V for more detail) > > Copyright 1987-2004, Larry Wall > > Perl may be copied only under the terms of either the Artistic > License or the > GNU General Public License, which may be found in the Perl 5 source > kit. > > Complete documentation for Perl, including FAQ lists, should be > found on > this system using `man perl' or `perldoc perl'. If you have access > to the > Internet, point your browser at http://www.perl.org/, the Perl Home > Page. > > > mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- > dbuser root --download true > > Can't locate object method "connect" via package "DBI" at / > bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 323. > ========================================== > > > Just for kicks, I thought it might be a permission issue, so I tried > it with sudo also, at least I got a different error: > > ================== > mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- > dbuser root --download true > > Password: > > Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/ > 5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/ > Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/ > Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/ > Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/ > 5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 / > Library/Perl/5.8.1 .) at /bioinformatics/pythonstuff/biosql-1.0.0/ > scripts/load_ncbi_taxonomy.pl line 195. > > BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/ > biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. > ===================== > > > (As for why I installed ActivePerl -- I don't remember, but it > seemed like a good idea at the time when I was installing various > packages and something or other requested or suggested the newer > version. I was a total noob at the time. Still am, sorta...) > > Nick > > > Hilmar Lapp wrote: >> Hi Nick, >> this is working fine for me, using perl v5.8.8. You may have >> noticed that DBI does have a method 'connect'. >> Your perl reports to be 5.10, and to have been built for Mac OSX, >> yet it is a binary from ActiveState. Is my interpretation correct >> that you installed this on top of or in place of Mac OSX's native >> perl v5.8.8? Correspondingly, are you sure that 'perl' (which is >> what you are calling below), /usr/bin/perl (which is what the >> script executes), and cpan all are the same perl? >> If this is all correct and all the right platform, could you try >> and edit the following code (starting at line 323): >> my $dbh = DBI->connect($dsn, >> $user, >> $pass, >> { RaiseError => 0, >> AutoCommit => 1, >> PrintError => 0, >> } >> ) or die $DBI::errstr; >> by removing the 'or die $DBI::errstr' part. This would be hoping >> that it's an incompatibility for v5.10. >> BTW are you sure you need perl 5.10? You will encounter various >> perl software that has not been tested against it yet (though I >> think Bioperl has been fixed meanwhile to be compatible). >> -hilmar >> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>> Hi all, >>> >>> (sorry that I cross-posted this to the biopython lis, I only just >>> realized I should get on the bioSQL list) >>> >>> >>> >>> I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy >>> ). I can get bioseqdb to work, and the biosql python scripts etc. >>> >>> However I can't get these directions to work in loading the >>> taxonomy database into bioseqdb. I get: "Can't locate object >>> method "connect" via package "DBI" " >>> >>> I double-checked to make sure I've got DBI in perl (see error >>> message below) but that doesn't seem to help. >>> >>> Any help appreciated! >>> Nick >>> >>> >>> >>> commands/returns: >>> =========================== >>> mws2:/bioinformatics/eg nick$ perl -v >>> >>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>> (with 3 registered patches, see perl -V for more detail) >>> >>> Copyright 1987-2007, Larry Wall >>> >>> Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com >>> Built Jan 10 2008 11:08:33 >>> >>> Perl may be copied only under the terms of either the Artistic >>> License or the >>> GNU General Public License, which may be found in the Perl 5 >>> source kit. >>> >>> Complete documentation for Perl, including FAQ lists, should be >>> found on >>> this system using "man perl" or "perldoc perl". If you have >>> access to the >>> Internet, point your browser at http://www.perl.org/, the Perl >>> Home Page. >>> >>> >>> >>> >>> >>> >>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>> Password: >>> >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /usr/local/Metadata >>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>> CPAN: LWP::UserAgent loaded ok (v5.810) >>> CPAN: Time::HiRes loaded ok (v1.9711) >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>> CPAN: YAML loaded ok (v0.66) >>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>> ............................................................................DONE >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>> Going to read /Users/nick/.cpan/sources/modules/ >>> 02packages.details.txt.gz >>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>> ............................................................................DONE >>> Fetching with LWP: >>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>> ............................................................................DONE >>> Going to write /usr/local/Metadata >>> DBI is up to date (1.607). >>> >>> >>> >>> >>> >>> >>> mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ >>> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >>> driver mysql --dbuser root --download true >>> >>> >>> Can't locate object method "connect" via package "DBI" at / >>> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >>> load_ncbi_taxonomy.pl line 323. >>> >>> mws2:/bioinformatics/eg nick$ >>> =========================== >>> >>> >>> >>> Additional sleuthing: >>> =========================== >>> Based on some web advice on this general error I also did this: >>> >>> sudo cpan DBD::mysql >>> >>> ...which did install something that wasn't installed. But the >>> same error resulted when the load_ncbi_taxonomy.pl script was run. >>> =========================== >>> >>> >>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >>> finding them in @INC or something doesn't seem to be the problem... >>> >>> (these commands return '1' if the module is successfully found) >>> ============ >>> perl -MDBD::mysql -e 'print 1' >>> 1 >>> >>> perl -MDBI -e 'print 1' >>> 1 >>> ============ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > ==================================================== > Nicholas J. Matzke > Ph.D. student, Graduate Student Researcher > Huelsenbeck Lab > Center for Theoretical Evolutionary Genomics > 4151 VLSB (Valley Life Sciences Building) > Department of Integrative Biology > University of California, Berkeley > > Lab websites: > http://ib.berkeley.edu/people/lab_detail.php?lab=54 > http://fisher.berkeley.edu/cteg/hlab.html > Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 > Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html > Lab phone: 510-643-6299 > Dept. fax: 510-643-6264 > Cell phone: 510-301-0179 > Email: matzke at berkeley.edu > > Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, > Ecology > VLSB 2013, Monday 1-1:30 (some TA there for all hours during work > week) > > Mailing address: > Department of Integrative Biology > 3060 VLSB #3140 > Berkeley, CA 94720-3140 > ==================================================== > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Sep 3 17:09:28 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Sep 2008 12:09:28 -0500 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Message-ID: <507AE529-1D58-44C9-A077-6A70A66DB5D3@illinois.edu> I'll give it a try; I have a locally built perl 5.10 on my laptop (Mac OS X). I know bioperl and bioperl-db work fine with perl 5.10, so maybe it is something with the script that is tripping things up. Maybe indirect object syntax ('new Class' instead of 'Class->new()')? The error looks similar to problems we have seen in the past which resolved when switching to the latter. chris On Sep 3, 2008, at 10:43 AM, Hilmar Lapp wrote: > Hi Nick, > > this is pretty weird. But the two different results between running > with and without sudo strongly indicate that something's wrong with > your perl installation setup. Specifically, DBI apparently isn't > installed, and the DBI module that you are picking up without the > sudo seems to be wrong or a corrupt one. > > You can ask perldoc for the full path to the module using the -l > argument: > > $ perldoc -l DBI > $ sudo perldoc -l DBI > $ /usr/bin/perldoc -l DBI > $ sudo /usr/bin/perldoc -l DBI > > should all yield the same result, and the following should, too: > > $ perl -e 'use DBI; $dbh=DBI- > >connect("dbi:mysql:database=test","","");' > > w/ and w/o using the full path, w/ and w/o prepending sudo. > > Is that what you are seeing? > > -hilmar > > On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > >> Hi Hilmar! >> >> Thanks, that's a good thought. But I just tried running it on the >> default 5.8.6 (I have MacOX 10.4), same result: >> >> >> ========================================== >> mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -v >> >> This is perl, v5.8.6 built for darwin-thread-multi-2level >> (with 4 registered patches, see perl -V for more detail) >> >> Copyright 1987-2004, Larry Wall >> >> Perl may be copied only under the terms of either the Artistic >> License or the >> GNU General Public License, which may be found in the Perl 5 source >> kit. >> >> Complete documentation for Perl, including FAQ lists, should be >> found on >> this system using `man perl' or `perldoc perl'. If you have access >> to the >> Internet, point your browser at http://www.perl.org/, the Perl Home >> Page. >> >> >> mws2:~ nick$ perl5.8.6 /bioinformatics/pythonstuff/biosql-1.0.0/ >> scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql -- >> dbuser root --download true >> >> Can't locate object method "connect" via package "DBI" at / >> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >> load_ncbi_taxonomy.pl line 323. >> ========================================== >> >> >> Just for kicks, I thought it might be a permission issue, so I >> tried it with sudo also, at least I got a different error: >> >> ================== >> mws2:~ nick$ sudo perl5.8.6 /bioinformatics/pythonstuff/ >> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >> driver mysql --dbuser root --download true >> >> Password: >> >> Can't locate DBI.pm in @INC (@INC contains: /System/Library/Perl/ >> 5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 / >> Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 / >> Library/Perl /Network/Library/Perl/5.8.6/darwin-thread- >> multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl / >> System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/ >> Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /bioinformatics/ >> pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. >> >> BEGIN failed--compilation aborted at /bioinformatics/pythonstuff/ >> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 195. >> ===================== >> >> >> (As for why I installed ActivePerl -- I don't remember, but it >> seemed like a good idea at the time when I was installing various >> packages and something or other requested or suggested the newer >> version. I was a total noob at the time. Still am, sorta...) >> >> Nick >> >> >> Hilmar Lapp wrote: >>> Hi Nick, >>> this is working fine for me, using perl v5.8.8. You may have >>> noticed that DBI does have a method 'connect'. >>> Your perl reports to be 5.10, and to have been built for Mac OSX, >>> yet it is a binary from ActiveState. Is my interpretation correct >>> that you installed this on top of or in place of Mac OSX's native >>> perl v5.8.8? Correspondingly, are you sure that 'perl' (which is >>> what you are calling below), /usr/bin/perl (which is what the >>> script executes), and cpan all are the same perl? >>> If this is all correct and all the right platform, could you try >>> and edit the following code (starting at line 323): >>> my $dbh = DBI->connect($dsn, >>> $user, >>> $pass, >>> { RaiseError => 0, >>> AutoCommit => 1, >>> PrintError => 0, >>> } >>> ) or die $DBI::errstr; >>> by removing the 'or die $DBI::errstr' part. This would be hoping >>> that it's an incompatibility for v5.10. >>> BTW are you sure you need perl 5.10? You will encounter various >>> perl software that has not been tested against it yet (though I >>> think Bioperl has been fixed meanwhile to be compatible). >>> -hilmar >>> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>>> Hi all, >>>> >>>> (sorry that I cross-posted this to the biopython lis, I only just >>>> realized I should get on the bioSQL list) >>>> >>>> >>>> >>>> I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy >>>> ). I can get bioseqdb to work, and the biosql python scripts etc. >>>> >>>> However I can't get these directions to work in loading the >>>> taxonomy database into bioseqdb. I get: "Can't locate object >>>> method "connect" via package "DBI" " >>>> >>>> I double-checked to make sure I've got DBI in perl (see error >>>> message below) but that doesn't seem to help. >>>> >>>> Any help appreciated! >>>> Nick >>>> >>>> >>>> >>>> commands/returns: >>>> =========================== >>>> mws2:/bioinformatics/eg nick$ perl -v >>>> >>>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>>> (with 3 registered patches, see perl -V for more detail) >>>> >>>> Copyright 1987-2007, Larry Wall >>>> >>>> Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com >>>> Built Jan 10 2008 11:08:33 >>>> >>>> Perl may be copied only under the terms of either the Artistic >>>> License or the >>>> GNU General Public License, which may be found in the Perl 5 >>>> source kit. >>>> >>>> Complete documentation for Perl, including FAQ lists, should be >>>> found on >>>> this system using "man perl" or "perldoc perl". If you have >>>> access to the >>>> Internet, point your browser at http://www.perl.org/, the Perl >>>> Home Page. >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>>> Password: >>>> >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /usr/local/Metadata >>>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>>> CPAN: LWP::UserAgent loaded ok (v5.810) >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>>> CPAN: YAML loaded ok (v0.66) >>>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>>> ............................................................................DONE >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>>> Going to read /Users/nick/.cpan/sources/modules/ >>>> 02packages.details.txt.gz >>>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>>> ............................................................................DONE >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>>> ............................................................................DONE >>>> Going to write /usr/local/Metadata >>>> DBI is up to date (1.607). >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ >>>> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- >>>> driver mysql --dbuser root --download true >>>> >>>> >>>> Can't locate object method "connect" via package "DBI" at / >>>> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ >>>> load_ncbi_taxonomy.pl line 323. >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> =========================== >>>> >>>> >>>> >>>> Additional sleuthing: >>>> =========================== >>>> Based on some web advice on this general error I also did this: >>>> >>>> sudo cpan DBD::mysql >>>> >>>> ...which did install something that wasn't installed. But the >>>> same error resulted when the load_ncbi_taxonomy.pl script was run. >>>> =========================== >>>> >>>> >>>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. >>>> not finding them in @INC or something doesn't seem to be the >>>> problem... >>>> >>>> (these commands return '1' if the module is successfully found) >>>> ============ >>>> perl -MDBD::mysql -e 'print 1' >>>> 1 >>>> >>>> perl -MDBI -e 'print 1' >>>> 1 >>>> ============ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> ==================================================== >> Nicholas J. Matzke >> Ph.D. student, Graduate Student Researcher >> Huelsenbeck Lab >> Center for Theoretical Evolutionary Genomics >> 4151 VLSB (Valley Life Sciences Building) >> Department of Integrative Biology >> University of California, Berkeley >> >> Lab websites: >> http://ib.berkeley.edu/people/lab_detail.php?lab=54 >> http://fisher.berkeley.edu/cteg/hlab.html >> Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 >> Lab personal page: http://fisher.berkeley.edu/cteg/members/ >> matzke.html >> Lab phone: 510-643-6299 >> Dept. fax: 510-643-6264 >> Cell phone: 510-301-0179 >> Email: matzke at berkeley.edu >> >> Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, >> Ecology >> VLSB 2013, Monday 1-1:30 (some TA there for all hours during work >> week) >> >> Mailing address: >> Department of Integrative Biology >> 3060 VLSB #3140 >> Berkeley, CA 94720-3140 >> ==================================================== >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From matzke at berkeley.edu Wed Sep 3 18:16:19 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 11:16:19 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> Message-ID: <48BED473.6070006@berkeley.edu> Hmm, I think you are onto something here...here is what I get with those commands: ========================================== mws2:~ nick$ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 3 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com Built Jan 10 2008 11:08:33 mws2:~ nick$ perldoc -V Perldoc v3.14_02, under perl v5.010000 for darwin mws2:~ nick$ perldoc -l DBI /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm mws2:~ nick$ sudo perldoc -l DBI Password: /usr/local/ActivePerl-5.10/site/lib/DBI.pm mws2:~ nick$ /usr/bin/perldoc -l DBI /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm mws2:~ nick$ sudo /usr/bin/perldoc -l DBI No documentation found for "DBI". mws2:~ nick$ perl -e 'use DBI; $dbh=DBI->connect("dbi:mysql:database=test","","");' Can't locate object method "connect" via package "DBI" (perhaps you forgot to load "DBI"?) at -e line 1. mws2:~ nick$ sudo perl -e 'use DBI; $dbh=DBI->connect("dbi:mysql:database=test","","");' [no text returned, so I guess this cmd worked] ========================================== Suggestions about what to do based on this? Thanks again! Nick Hilmar Lapp wrote: > Hi Nick, > > this is pretty weird. But the two different results between running with > and without sudo strongly indicate that something's wrong with your perl > installation setup. Specifically, DBI apparently isn't installed, and > the DBI module that you are picking up without the sudo seems to be > wrong or a corrupt one. > > You can ask perldoc for the full path to the module using the -l argument: > > $ perldoc -l DBI > $ sudo perldoc -l DBI > $ /usr/bin/perldoc -l DBI > $ sudo /usr/bin/perldoc -l DBI > > should all yield the same result, and the following should, too: > > $ perl -e 'use DBI; > $dbh=DBI->connect("dbi:mysql:database=test","","");' > > w/ and w/o using the full path, w/ and w/o prepending sudo. > > Is that what you are seeing? > > -hilmar > > On Sep 2, 2008, at 11:57 PM, Nick Matzke wrote: > >> Hi Hilmar! >> >> Thanks, that's a good thought. But I just tried running it on the >> default 5.8.6 (I have MacOX 10.4), same result: >> >> >> ========================================== >> mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1' >> 1 >> >> mws2:~ nick$ perl5.8.6 -v >> >> This is perl, v5.8.6 built for darwin-thread-multi-2level >> (with 4 registered patches, see perl -V for more detail) >> >> Copyright 1987-2004, Larry Wall >> >> Perl may be copied only under the terms of either the Artistic License >> or the >> GNU General Public License, which may be found in the Perl 5 source kit. >> >> Complete documentation for Perl, including FAQ lists, should be found on >> this system using `man perl' or `perldoc perl'. If you have access to >> the >> Internet, point your browser at http://www.perl.org/, the Perl Home Page. >> >> >> mws2:~ nick$ perl5.8.6 >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> Can't locate object method "connect" via package "DBI" at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 323. >> ========================================== >> >> >> Just for kicks, I thought it might be a permission issue, so I tried >> it with sudo also, at least I got a different error: >> >> ================== >> mws2:~ nick$ sudo perl5.8.6 >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> --dbname bioseqdb --driver mysql --dbuser root --download true >> >> Password: >> >> Can't locate DBI.pm in @INC (@INC contains: >> /System/Library/Perl/5.8.6/darwin-thread-multi-2level >> /System/Library/Perl/5.8.6 >> /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 >> /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level >> /Network/Library/Perl/5.8.6 /Network/Library/Perl >> /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level >> /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 195. >> >> BEGIN failed--compilation aborted at >> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >> line 195. >> ===================== >> >> >> (As for why I installed ActivePerl -- I don't remember, but it seemed >> like a good idea at the time when I was installing various packages >> and something or other requested or suggested the newer version. I >> was a total noob at the time. Still am, sorta...) >> >> Nick >> >> >> Hilmar Lapp wrote: >>> Hi Nick, >>> this is working fine for me, using perl v5.8.8. You may have noticed >>> that DBI does have a method 'connect'. >>> Your perl reports to be 5.10, and to have been built for Mac OSX, yet >>> it is a binary from ActiveState. Is my interpretation correct that >>> you installed this on top of or in place of Mac OSX's native perl >>> v5.8.8? Correspondingly, are you sure that 'perl' (which is what you >>> are calling below), /usr/bin/perl (which is what the script >>> executes), and cpan all are the same perl? >>> If this is all correct and all the right platform, could you try and >>> edit the following code (starting at line 323): >>> my $dbh = DBI->connect($dsn, >>> $user, >>> $pass, >>> { RaiseError => 0, >>> AutoCommit => 1, >>> PrintError => 0, >>> } >>> ) or die $DBI::errstr; >>> by removing the 'or die $DBI::errstr' part. This would be hoping that >>> it's an incompatibility for v5.10. >>> BTW are you sure you need perl 5.10? You will encounter various perl >>> software that has not been tested against it yet (though I think >>> Bioperl has been fixed meanwhile to be compatible). >>> -hilmar >>> On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote: >>>> Hi all, >>>> >>>> (sorry that I cross-posted this to the biopython lis, I only just >>>> realized I should get on the bioSQL list) >>>> >>>> >>>> >>>> I'm following the BioSQL tutorial at the biopython website >>>> (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ). I can get >>>> bioseqdb to work, and the biosql python scripts etc. >>>> >>>> However I can't get these directions to work in loading the taxonomy >>>> database into bioseqdb. I get: "Can't locate object method >>>> "connect" via package "DBI" " >>>> >>>> I double-checked to make sure I've got DBI in perl (see error >>>> message below) but that doesn't seem to help. >>>> >>>> Any help appreciated! >>>> Nick >>>> >>>> >>>> >>>> commands/returns: >>>> =========================== >>>> mws2:/bioinformatics/eg nick$ perl -v >>>> >>>> This is perl, v5.10.0 built for darwin-thread-multi-2level >>>> (with 3 registered patches, see perl -V for more detail) >>>> >>>> Copyright 1987-2007, Larry Wall >>>> >>>> Binary build 1002 [283697] provided by ActiveState >>>> http://www.ActiveState.com >>>> Built Jan 10 2008 11:08:33 >>>> >>>> Perl may be copied only under the terms of either the Artistic >>>> License or the >>>> GNU General Public License, which may be found in the Perl 5 source >>>> kit. >>>> >>>> Complete documentation for Perl, including FAQ lists, should be >>>> found on >>>> this system using "man perl" or "perldoc perl". If you have access >>>> to the >>>> Internet, point your browser at http://www.perl.org/, the Perl Home >>>> Page. >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ sudo cpan DBI >>>> Password: >>>> >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /usr/local/Metadata >>>> Database was generated on Wed, 23 Jul 2008 10:02:50 GMT >>>> CPAN: LWP::UserAgent loaded ok (v5.810) >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz >>>> CPAN: YAML loaded ok (v0.66) >>>> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz >>>> ............................................................................DONE >>>> >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz >>>> Going to read >>>> /Users/nick/.cpan/sources/modules/02packages.details.txt.gz >>>> Database was generated on Mon, 01 Sep 2008 10:02:51 GMT >>>> ............................................................................DONE >>>> >>>> Fetching with LWP: >>>> http://ppm.activestate.com/CPAN/modules/03modlist.data.gz >>>> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz >>>> ............................................................................DONE >>>> >>>> Going to write /usr/local/Metadata >>>> DBI is up to date (1.607). >>>> >>>> >>>> >>>> >>>> >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >>>> --dbname bioseqdb --driver mysql --dbuser root --download true >>>> >>>> >>>> Can't locate object method "connect" via package "DBI" at >>>> /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl >>>> line 323. >>>> >>>> mws2:/bioinformatics/eg nick$ >>>> =========================== >>>> >>>> >>>> >>>> Additional sleuthing: >>>> =========================== >>>> Based on some web advice on this general error I also did this: >>>> >>>> sudo cpan DBD::mysql >>>> >>>> ...which did install something that wasn't installed. But the same >>>> error resulted when the load_ncbi_taxonomy.pl script was run. >>>> =========================== >>>> >>>> >>>> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not >>>> finding them in @INC or something doesn't seem to be the problem... >>>> >>>> (these commands return '1' if the module is successfully found) >>>> ============ >>>> perl -MDBD::mysql -e 'print 1' >>>> 1 >>>> >>>> perl -MDBI -e 'print 1' >>>> 1 >>>> ============ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> ==================================================== >> Nicholas J. Matzke >> Ph.D. student, Graduate Student Researcher >> Huelsenbeck Lab >> Center for Theoretical Evolutionary Genomics >> 4151 VLSB (Valley Life Sciences Building) >> Department of Integrative Biology >> University of California, Berkeley >> >> Lab websites: >> http://ib.berkeley.edu/people/lab_detail.php?lab=54 >> http://fisher.berkeley.edu/cteg/hlab.html >> Dept. personal page: >> http://ib.berkeley.edu/people/students/person_detail.php?person=370 >> Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html >> Lab phone: 510-643-6299 >> Dept. fax: 510-643-6264 >> Cell phone: 510-301-0179 >> Email: matzke at berkeley.edu >> >> Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology >> VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) >> >> Mailing address: >> Department of Integrative Biology >> 3060 VLSB #3140 >> Berkeley, CA 94720-3140 >> ==================================================== >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From matzke at berkeley.edu Wed Sep 3 22:44:54 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 15:44:54 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BED473.6070006@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> Message-ID: <48BF1366.1020407@berkeley.edu> Well, I'm not sure what I did, but some combination of these things seems to have worked. Your guess is as good as mine... 1. moved the site/lib directory (which contains DBI.pm) to the front of my PERL5LIB (which goes into @INC) export PERL5LIB=$PERL5LIB:/usr/local/ActivePerl-5.10/site/lib:/usr/local/ActivePerl-5.10/man/man3:/usr/local/ActivePerl-5.10/site/lib/Bundle 2. Checked to make sure DBI & DBD::mysql were installed ========================================== mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl -MCPAN -e 'install DBI' CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Mon, 01 Sep 2008 10:02:51 GMT DBI is up to date (1.607). mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl -MCPAN -e 'install DBD::mysql' CPAN: Storable loaded ok (v2.18) Going to read /usr/local/Metadata Database was generated on Mon, 01 Sep 2008 10:02:51 GMT DBD::mysql is up to date (4.008). ========================================== 3. (Make sure you have an empty version of the db, at least for me I got errors if I had already loaded sequences etc. into it...I got errors like this: ========================================== note: node (28;331111;27;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (70;300268;69;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (77;3002 ========================================== 4. Ran it again: (I also added '--host localhost') mws2:/usr/local/ActivePerl-5.10/bin nick$ sudo perl /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true --host localhost Loading NCBI taxon database in taxdata: ... retrieving all taxon nodes in the database ... reading in taxon nodes from nodes.dmp ... insert / update / delete taxon nodes ... (committing nodes) ... rebuilding nested set left/right values ... reading in taxon names from names.dmp ... deleting old taxon names ... inserting new taxon names ... cleaning up Done. So thanks for the help, something or other worked! Cheers, Nick From hlapp at gmx.net Wed Sep 3 22:50:04 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 18:50:04 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BED473.6070006@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> Message-ID: <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote: > [...] > mws2:~ nick$ perldoc -l DBI > > /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm Can you pull up this file in an editor and see what's in there? I think this may just be the CPAN bundle definition (which modules to install together), but not the actual DBI module itself. > > mws2:~ nick$ sudo perldoc -l DBI > Password: > > /usr/local/ActivePerl-5.10/site/lib/DBI.pm If you inspect this one, it will probably be the actual DBI module. So I suspect that your Perl module search paths aren't the same between executing as root or not. If you do 'perl -V' (capital-v) you will see the include path array (@INC) printed at the end. It should be identical whether under sudo or not, but I suspect that for you it will not be the same. If that's indeed the case then the question is why is the path different. As the one for you as normal user is wrong, you can look into your shell initialization files (.tcshrc, .cshrc for csh/ tcsh; .profile, .bash_profile, .login for bash) whether you see anything there that aims to mess with PERL5LIB. Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Sep 3 23:13:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 3 Sep 2008 19:13:48 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF1366.1020407@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> Message-ID: <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> On Sep 3, 2008, at 6:44 PM, Nick Matzke wrote: > Well, I'm not sure what I did, but some combination of these things > seems to have worked. Great we got you going! > [...] > 3. (Make sure you have an empty version of the db, at least for me I > got errors if I had already loaded sequences etc. into it...I got > errors like this: > > ========================================== > note: node (28;331111;27;species;;) is retired; failed to delete: > Cannot delete or update a parent row: a foreign key constraint fails > (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY > (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (70;300268;69;species;;) is retired; failed to delete: > Cannot delete or update a parent row: a foreign key constraint fails > (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY > (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (77;3002 > ========================================== > These aren't fatal, right? What is basically means is that your sequences referenced taxa that are not yet or not anymore in the NCBI taxonomy download. The script doesn't yet process the change log that NCBI also produces. So if two nodes get merged into one, or one gets split into two new, the script can't migrate the data that you already have. Nodes that are in the database but not in the taxonomy dump from NCBI will be considered retired, and the script tries to delete them if there aren't any sequences yet pointing to them. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From matzke at berkeley.edu Thu Sep 4 01:10:16 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 18:10:16 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> Message-ID: <48BF3578.9000806@berkeley.edu> I know my issue is fixed, but just for completeness... Hilmar Lapp wrote: > > On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote: > >> [...] >> mws2:~ nick$ perldoc -l DBI >> >> /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm > > Can you pull up this file in an editor and see what's in there? I think > this may just be the CPAN bundle definition (which modules to install > together), but not the actual DBI module itself. > >> >> mws2:~ nick$ sudo perldoc -l DBI >> Password: >> >> /usr/local/ActivePerl-5.10/site/lib/DBI.pm > > If you inspect this one, it will probably be the actual DBI module. > > So I suspect that your Perl module search paths aren't the same between > executing as root or not. If you do 'perl -V' (capital-v) you will see > the include path array (@INC) printed at the end. It should be identical > whether under sudo or not, but I suspect that for you it will not be the > same. This was indeed true. I couldn't figure out how to fix it though. It appears that sudo doesn't read the .bash_profile file where I have additions to the PERL5LIB environmental variable. Do you know of a way to get sudo to read the standard environmental variables or something like that? Cheers! Thanks again for the help! Nick > If that's indeed the case then the question is why is the path > different. As the one for you as normal user is wrong, you can look into > your shell initialization files (.tcshrc, .cshrc for csh/tcsh; .profile, > .bash_profile, .login for bash) whether you see anything there that aims > to mess with PERL5LIB. > > Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same. > > -hilmar > -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From matzke at berkeley.edu Thu Sep 4 01:11:47 2008 From: matzke at berkeley.edu (Nick Matzke) Date: Wed, 03 Sep 2008 18:11:47 -0700 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> Message-ID: <48BF35D3.9040303@berkeley.edu> Hilmar Lapp wrote: > > On Sep 3, 2008, at 6:44 PM, Nick Matzke wrote: > >> Well, I'm not sure what I did, but some combination of these things >> seems to have worked. > > Great we got you going! > >> [...] >> 3. (Make sure you have an empty version of the db, at least for me I >> got errors if I had already loaded sequences etc. into it...I got >> errors like this: >> >> ========================================== >> note: node (28;331111;27;species;;) is retired; failed to delete: >> Cannot delete or update a parent row: a foreign key constraint fails >> (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY >> (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) >> note: node (70;300268;69;species;;) is retired; failed to delete: >> Cannot delete or update a parent row: a foreign key constraint fails >> (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY >> (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) >> note: node (77;3002 >> ========================================== >> > > These aren't fatal, right? What is basically means is that your > sequences referenced taxa that are not yet or not anymore in the NCBI > taxonomy download. Those weren't fatal, but eventually I hit this and it crashed: ========================================== note: node (4484;312017;4483;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) note: node (4490;324602;4489;species;;) is retired; failed to delete: Cannot delete or update a parent row: a foreign key constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) failed to insert node (4577;4577;4575;species;1;1): Duplicate entry '4577' for key 2 at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl line 581. ========================================== ...but like I said it worked fine on an empty database which was fine for my purposes. Thanks! > > The script doesn't yet process the change log that NCBI also produces. > So if two nodes get merged into one, or one gets split into two new, the > script can't migrate the data that you already have. Nodes that are in > the database but not in the taxonomy dump from NCBI will be considered > retired, and the script tries to delete them if there aren't any > sequences yet pointing to them. > > -hilmar -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: matzke at berkeley.edu Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week) Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 ==================================================== From dicknetherlands at gmail.com Mon Sep 1 13:47:01 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Mon, 1 Sep 2008 14:47:01 +0100 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence In-Reply-To: <48BBEF08.8060402@gmx.net> References: <48BBEF08.8060402@gmx.net> Message-ID: You raise two points in this email. The second one, which is easier to deal with, I'll answer first! Bascially yes please do file a bug report about the unique identifiers for features not getting reset on new sequences, using Bugzilla at biojava.org. Now the first one, which relates to your stack trace. Mid way through the stacktrace you see this line: Caused by: java.lang.OutOfMemoryError: Java heap space Basically you're loading loads of stuff into memory and so you're running out of it. Java 5 by default allocates no less than 1/64th and no more than 1/4th of the machine's memory to your program, which you can increase using the -Xms and -Xmx params when starting up your JVM (e.g. when you type the java comand to start your program). Increasing these params will help prevent out of memory messages, particularly if you are dealing with very large sequences. See this link for info on the -Xms and -Xmx options and how they work in various different environments (command line, Tomcat, Eclipse, etc.): http://javahowto.blogspot.com/2006/06/6-common-errors-in-setting-java-heap.html cheers, Richard 2008/9/1 Gabrielle Doan : > Hi Richard, > thanks a lot for your answer. I've changed the size of the rank in the > BioSQL table seqfeature from smallint unsigned to int unsigned. So that the > error messages because of the rank do not occur anymore. > But now I'm facing an other problem. If I try to insert a new feature to > human chromosome 1 and 2 into my database I get following message: > > org.hibernate.PropertyAccessException: Exception occurred inside getter of > org.biojavax.bio.seq.SimpleRichSequence.stringSequence > at > org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:148) > at > org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:256) > at > org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:209) > at > org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:3581) > at > org.hibernate.event.def.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:167) > at > org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:120) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:196) > at > org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:76) > at > org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) > at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) > at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) > at > org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) > at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) > at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) > at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:145) > ... 14 more > Caused by: java.lang.OutOfMemoryError: Java heap space > at java.util.Arrays.copyOf(Arrays.java:2882) > at > java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100) > at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:572) > at java.lang.StringBuffer.append(StringBuffer.java:320) > at > org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTokenization.java:214) > at > org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenizeSymbolList(AlphabetManager.java:1460) > at > org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:102) > at > org.biojavax.bio.seq.DummyRichSequenceHandler.seqString(DummyRichSequenceHandler.java:115) > at > org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.seqString(BioSQLRichSequenceHandler.java:155) > at > org.biojavax.bio.seq.ThinRichSequence.seqString(ThinRichSequence.java:188) > at > org.biojavax.bio.seq.SimpleRichSequence.getStringSequence(SimpleRichSequence.java:77) > ... 19 more > > I also had a conversation with Hilmar Lapp, who told me that there's > possibly a bug in BioJava because the unique property does hold for the four > elements bioentry_id, type_term_id, source_term_id and rank but it seems > that BioJava always inkrements the rank for each new feature. Should I post > a bug report? > > It would be very nice if you could help me. I am grateful for any > hints. Thanks a lot. > > cheers > Gabrielle > > > > > > -------- Original-Nachricht -------- > Betreff: Re: [Biojava-l] Problems with adding miRNA to sequence > Datum: Thu, 28 Aug 2008 23:45:35 +0100 > Von: Richard Holland > An: Gabrielle Doan > CC: biojava-l at biojava.org > Referenzen: <48B6B354.6010307 at gmx.net> > > Looks like your sequence has so many features that it exceeds the > maximum permitted by BioSQL: > > com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of > range value adjusted for column 'rank' at row 1 > > Not sure what you can do about this other than go to the Feature table > in your database and increase the maximum value allowed in the 'rank' > column. > > cheers, > Richard > > > 2008/8/28 Gabrielle Doan : >> >> Hi all, >> I would like to insert new features (miRNA) into my exitsting BioSQL >> database. At the moment the database contains the chromosomes 1-22, X, Y >> and MT downloaded from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/. And >> now I have tried to add the information about miRNA from >> http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl into my >> database with following code: >> >> private void makeAFeature(String id, String chr, int startpos, >> int endpos, Strand strand, float score, String gene) >> throws ChangeVetoExceptionIllegalSymbolException >> { >> RichSequence rs = chromosomes.get(chr); >> if (rs == null) { >> rs = db.SearchForSequence(chr); >> chromosomes.put(chr, rs); >> } >> RichFeature feat = RichFeature.Tools.makeEmptyFeature(); >> feat.setName(id); >> RichLocation rl = new SimpleRichLocation(new >> >> SimplePosition(startpos),new SimplePosition(endpos), >> 1,strand); >> feat.setLocation(rl); >> try { >> >> feat.setTypeTerm(RichObjectFactory.getDefaultOntology() >> .getOrCreateTerm("miRNA")); >> feat.setType(feat.getTypeTerm().getName()); >> } catch (InvalidTermException e) { >> // TODO Auto-generated catch block >> e.printStackTrace(); >> } >> feat.getAnnotation().setProperty("score", >> Float.valueOf(score)); >> feat.getAnnotation().setProperty("gene", gene); >> feat.setParent(rs); >> rs.getFeatureSet().add(feat); >> } >> >> I successfully inserted the information for chromosome 3-22, X, Y and MT. >> But when I try to deal with chromosome 1, 2 in the same way I get >> following message: >> >> org.hibernate.exception.DataException: could not insert: [Feature] >> at >> >> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) >> at >> >> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) >> at >> >> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40) >> at >> >> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163) >> at >> >> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643) >> at >> >> org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51) >> at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181) >> at >> >> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94) >> at >> >> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70) >> at >> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507) >> at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499) >> at >> org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218) >> at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268) >> at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216) >> at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) >> at >> org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296) >> at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242) >> at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219) >> at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169) >> at org.hibernate.engine.Cascade.cascade(Cascade.java:130) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122) >> at >> >> org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65) >> at >> >> org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26) >> at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) >> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) >> at >> org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) >> at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254) >> at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220) >> at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57) >> Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of >> range value adjusted for column 'rank' at row 1 >> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973) >> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) >> at >> >> com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129) >> at >> >> com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283) >> at >> >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268) >> at >> >> org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73) >> at >> >> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33) >> ... 32 more >> >> It would be very nice if someone could help me. I am grateful for any >> hints. Thanks a lot. >> >> Cheers, >> Gabrielle >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -- > Richard Holland > Finance Director > Eagle Genomics > http://www.eaglegenomics.com/ > > -- Richard Holland Finance Director Eagle Genomics http://www.eaglegenomics.com/ From hlapp at gmx.net Thu Sep 4 14:07:44 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:07:44 -0400 Subject: [BioSQL-l] [Biojava-l] Problems with adding miRNA to sequence In-Reply-To: References: <48BBEF08.8060402@gmx.net> Message-ID: On Sep 1, 2008, at 9:47 AM, Richard Holland wrote: > Bascially yes please do file a bug report about the unique > identifiers for features not getting reset on new sequences Just for clarification, the bug appears to be not to reset the rank for every new combination of feature type and source terms, for the same sequence. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Sep 4 14:25:16 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:25:16 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF3578.9000806@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <60AFD92C-21C1-4427-A7F8-E5F8970EA9C3@gmx.net> <48BF3578.9000806@berkeley.edu> Message-ID: On Sep 3, 2008, at 9:10 PM, Nick Matzke wrote: > Do you know of a way to get sudo to read the standard environmental > variables or something like that? You can put them in the shell initialization files of the target user (root in your examples). Note that sudo will remove the PERL5LIB, PERLLIB, and PERLOPT environment variables when invoked, so as it turns out that invoking perl w/ and w/o sudo isn't the same is actually by design if you have have PERL5LIB changed for your local user. In reality there should rarely if ever be a need to use sudo when running a biosql, bioperl-db, or bioperl perl script. Are you sure you need to do this? The reason you saw the problems were most likely because the directory //Bundle was in PERL5LIB, and was so relatively at the front. I doubt that it needs to be there to begin with; have you observed any failures or problems if you remove that directory completely? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Sep 4 14:28:37 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Sep 2008 10:28:37 -0400 Subject: [BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb In-Reply-To: <48BF35D3.9040303@berkeley.edu> References: <48BDD1B2.80407@berkeley.edu> <48BE0B0E.6040604@berkeley.edu> <8FE95BD9-F1B2-48A5-A86E-26910820AC00@gmx.net> <48BED473.6070006@berkeley.edu> <48BF1366.1020407@berkeley.edu> <468085BE-8641-480B-8644-A69C5CAD7EB1@gmx.net> <48BF35D3.9040303@berkeley.edu> Message-ID: <46C49E37-B9F1-4009-9E16-A976582908ED@gmx.net> On Sep 3, 2008, at 9:11 PM, Nick Matzke wrote: > Those weren't fatal, but eventually I hit this and it crashed: > > ========================================== > note: node (4484;312017;4483;species;;) is retired; failed to > delete: Cannot delete or update a parent row: a foreign key > constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` > FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > note: node (4490;324602;4489;species;;) is retired; failed to > delete: Cannot delete or update a parent row: a foreign key > constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry` > FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`)) > failed to insert node (4577;4577;4575;species;1;1): Duplicate entry > '4577' for key 2 at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/ > load_ncbi_taxonomy.pl line 581. > ========================================== > > ...but like I said it worked fine on an empty database which was > fine for my purposes. I think this might be fixed in BioSQL v1.0.1. (v1.0.1 fixes the load_ncbi_taxonomy.pl script to no longer assume or require the primary key and the NCBI taxonID be identical, which I think is the reason the failing insert above was an insert rather than the update it should have been). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From tatedger at googlemail.com Thu Sep 25 15:23:46 2008 From: tatedger at googlemail.com (john paul) Date: Thu, 25 Sep 2008 16:23:46 +0100 Subject: [BioSQL-l] Can't locate object method "get_dbxrefs" Message-ID: Hello guys, I need to pick your brain on this. I was trying to load some sequences in a fresh RH build using bioperl-db and got the following error: [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost --dbuser root --dbname biosql --namespace swissprot --format swiss /home/tatedger/tmp/uniprot_sprot.dat --testonly Loading /home/tatedger/tmp/uniprot_sprot.dat ... Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line 552, line 70. I have seen some posts on this regard ( http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but it wasn't clear to me what the solution would be. My configuration: - mysql version 4.1.7 - Red Hat Enterprise Linux ES release 4 (Nahant) to install bioperl and bioperl-db I used the help found on the website following - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. bioperl-db test 04 shows the same error. [tatedger at localhost bioperl-db]$ perl t/04swiss.t 1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line 552, line 78. my @INC file looks like /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl What am I doing wrong? Could you help? Thanks in advance for your help Tom From tatedger at googlemail.com Thu Sep 25 16:27:29 2008 From: tatedger at googlemail.com (john paul) Date: Thu, 25 Sep 2008 17:27:29 +0100 Subject: [BioSQL-l] [Bioperl-l] Can't locate object method "get_dbxrefs" In-Reply-To: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> References: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> Message-ID: On Thu, Sep 25, 2008 at 4:40 PM, Brian Osborne wrote: > John, > > What does: > > >locate Bio/Ontology/Term.pm > > Say? > Silly me. $ locate Bio/Ontology/Term.pm /usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm and $ cat /usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm|grep get_dbxrefs produced no answer the latest version posted by Sendu on cpan says for that module # $Id: Term.pm,v 1.31.4.1 2006/10/02 23:10:22 sendu Exp $ # # BioPerl module for Bio::Ontology::Term and the live version at ( http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/Ontology/Term.pm ) says # $Id: Term.pm 14708 2008-06-10 00:08:17Z heikki $ # # BioPerl module for Bio::Ontology::Term # I was using an old distribution from CPAN. reinstalling from the main trunk svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live solved the problem. Thanks again Tom > > Brian O. > > > > On Sep 25, 2008, at 11:23 AM, john paul wrote: > > Hello guys, >> >> I need to pick your brain on this. I was trying to load some sequences in >> a >> fresh RH build using bioperl-db and got the following error: >> >> [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost >> --dbuser root --dbname biosql --namespace swissprot --format swiss >> /home/tatedger/tmp/uniprot_sprot.dat --testonly >> Loading /home/tatedger/tmp/uniprot_sprot.dat ... >> Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via >> package >> "Bio::Ontology::Term" at >> /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line >> 552, line 70. >> >> >> I have seen some posts on this regard ( >> http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but it >> wasn't >> clear to me what the solution would be. >> >> >> My configuration: >> - mysql version 4.1.7 >> - Red Hat Enterprise Linux ES release 4 (Nahant) >> >> to install bioperl and bioperl-db I used the help found on the website >> following >> - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz >> - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db >> - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. >> >> bioperl-db test 04 shows the same error. >> >> [tatedger at localhost bioperl-db]$ perl t/04swiss.t >> 1..52 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term" >> at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm >> line >> 552, line 78. >> >> >> my @INC file looks like >> /usr/lib/perl5/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/5.8.5 >> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >> /usr/lib/perl5/site_perl/5.8.5 >> /usr/lib/perl5/site_perl/5.8.4 >> /usr/lib/perl5/site_perl/5.8.3 >> /usr/lib/perl5/site_perl/5.8.2 >> /usr/lib/perl5/site_perl/5.8.1 >> /usr/lib/perl5/site_perl/5.8.0 >> /usr/lib/perl5/site_perl >> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.5 >> /usr/lib/perl5/vendor_perl/5.8.4 >> /usr/lib/perl5/vendor_perl/5.8.3 >> /usr/lib/perl5/vendor_perl/5.8.2 >> /usr/lib/perl5/vendor_perl/5.8.1 >> /usr/lib/perl5/vendor_perl/5.8.0 >> /usr/lib/perl5/vendor_perl >> >> What am I doing wrong? Could you help? >> >> Thanks in advance for your help >> Tom >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From biopython at maubp.freeserve.co.uk Fri Sep 26 13:56:24 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 26 Sep 2008 14:56:24 +0100 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? Message-ID: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Hi All, In BioSQL v1.0.1, fields bioentry.accession and dbxref.accession were increased from 40 to 128 characters. See http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html However, bioentry.name and bioentry.identifier are still only 40 characters - which seems a bit short, given that BioPerl's load_seqdatabase.pl seems to put the full contents of a FASTA identifier (up to the first space) in both bioentry.name and bioentry.identifier fields. I've just been dealing with Biopython and loading FASTA files into BioSQL (Bug 2425) and a similar concern applies here. Has anyone had any real world problems with the bioentry.name and bioentry.identifier fields being too small? Peter From hlapp at gmx.net Fri Sep 26 14:24:57 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 26 Sep 2008 10:24:57 -0400 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Message-ID: Interesting. I see your logic and I guess you have a point. I've almost exclusively been loading all kinds of genbank, {swiss,uni}prot, unigene etc files, which don't suffer from this problem, as the name then is either identical to the accession, or is a short gene symbol, and the identifier is the GI#, or empty. I myself wouldn't load FASTA files w/o any processing/parsing the identifier token, but maybe that's not a reasonable expectation to put on everyone else? -hilmar On Sep 26, 2008, at 9:56 AM, Peter wrote: > Hi All, > > In BioSQL v1.0.1, fields bioentry.accession and dbxref.accession were > increased from 40 to 128 characters. See > http://lists.open-bio.org/pipermail/biosql-l/2008-August/001311.html > > However, bioentry.name and bioentry.identifier are still only 40 > characters - which seems a bit short, given that BioPerl's > load_seqdatabase.pl seems to put the full contents of a FASTA > identifier (up to the first space) in both bioentry.name and > bioentry.identifier fields. I've just been dealing with Biopython and > loading FASTA files into BioSQL (Bug 2425) and a similar concern > applies here. > > Has anyone had any real world problems with the bioentry.name and > bioentry.identifier fields being too small? > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Fri Sep 26 14:46:19 2008 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 26 Sep 2008 15:46:19 +0100 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> Message-ID: <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> On Fri, Sep 26, 2008 at 3:24 PM, Hilmar Lapp wrote: > > Interesting. I see your logic and I guess you have a point. > > I've almost exclusively been loading all kinds of genbank, {swiss,uni}prot, > unigene etc files, which don't suffer from this problem, as the name then is > either identical to the accession, or is a short gene symbol, and the > identifier is the GI#, or empty. In my case its also been mostly GenBank files, where long names are not an issue. > I myself wouldn't load FASTA files w/o any processing/parsing the identifier > token, but maybe that's not a reasonable expectation to put on everyone > else? I think is not unreasonable to want to import FASTA files directly (but this is not something I've actually done other than for testing). For example, I might want to import NCBI FASTA files directly, but these probably have names under 40 letters. Another example would be sequencing or assembly output, but I don't have a feel for what kind of length names are used here. I was half expecting someone on the list to say "Oh yes - we had to increase the field size when we were importing XYZ". Peter From barry.moore at genetics.utah.edu Fri Sep 26 15:00:51 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 26 Sep 2008 09:00:51 -0600 Subject: [BioSQL-l] bioentry.name and bioentry.identifier only 40 characters? In-Reply-To: <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> References: <320fb6e00809260656r2813f729m3a639ec9803c86b0@mail.gmail.com> <320fb6e00809260746p14503c5en2ea02dbe9d88b30c@mail.gmail.com> Message-ID: I've tweaked some of those varchars in the past on local installations, but I can't remember off the top of my head if I did that for name - probably not. I would to agree with the emerging view though - I don't know that I would need longer names right now, but it hardly makes sense to have an accession length of 128 and a name length of 40 since the name may well be or include the accession. B Barry Moore Senior Research Specialist Eccles Institute of Human Genetics Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 On Sep 26, 2008, at 8:46 AM, Peter wrote: > On Fri, Sep 26, 2008 at 3:24 PM, Hilmar Lapp wrote: >> >> Interesting. I see your logic and I guess you have a point. >> >> I've almost exclusively been loading all kinds of genbank, >> {swiss,uni}prot, >> unigene etc files, which don't suffer from this problem, as the >> name then is >> either identical to the accession, or is a short gene symbol, and the >> identifier is the GI#, or empty. > > In my case its also been mostly GenBank files, where long names are > not an issue. > >> I myself wouldn't load FASTA files w/o any processing/parsing the >> identifier >> token, but maybe that's not a reasonable expectation to put on >> everyone >> else? > > I think is not unreasonable to want to import FASTA files directly > (but this > is not something I've actually done other than for testing). For > example, > I might want to import NCBI FASTA files directly, but these > probably have > names under 40 letters. Another example would be sequencing or > assembly > output, but I don't have a feel for what kind of length names are > used here. > > I was half expecting someone on the list to say "Oh yes - we had to > increase > the field size when we were importing XYZ". > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From bosborne11 at verizon.net Thu Sep 25 15:40:45 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 25 Sep 2008 11:40:45 -0400 Subject: [BioSQL-l] [Bioperl-l] Can't locate object method "get_dbxrefs" In-Reply-To: References: Message-ID: <2A46D690-D925-4188-9DDF-468E31CE83BE@verizon.net> John, What does: >locate Bio/Ontology/Term.pm Say? Brian O. On Sep 25, 2008, at 11:23 AM, john paul wrote: > Hello guys, > > I need to pick your brain on this. I was trying to load some > sequences in a > fresh RH build using bioperl-db and got the following error: > > [tatedger at localhost biosql]$ perl load_seqdatabase.pl --host localhost > --dbuser root --dbname biosql --namespace swissprot --format swiss > /home/tatedger/tmp/uniprot_sprot.dat --testonly > Loading /home/tatedger/tmp/uniprot_sprot.dat ... > Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via > package > "Bio::Ontology::Term" at > /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm > line > 552, line 70. > > > I have seen some posts on this regard ( > http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but > it wasn't > clear to me what the solution would be. > > > My configuration: > - mysql version 4.1.7 > - Red Hat Enterprise Linux ES release 4 (Nahant) > > to install bioperl and bioperl-db I used the help found on the website > following > - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz > - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db > - biosql schema is loaded and load_ncbi_taxonomy.pl worked fine. > > bioperl-db test 04 shows the same error. > > [tatedger at localhost bioperl-db]$ perl t/04swiss.t > 1..52 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > Can't locate object method "get_dbxrefs" via package > "Bio::Ontology::Term" > at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/ > PersistentObject.pm line > 552, line 78. > > > my @INC file looks like > /usr/lib/perl5/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/5.8.5 > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.5 > /usr/lib/perl5/site_perl/5.8.4 > /usr/lib/perl5/site_perl/5.8.3 > /usr/lib/perl5/site_perl/5.8.2 > /usr/lib/perl5/site_perl/5.8.1 > /usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.5 > /usr/lib/perl5/vendor_perl/5.8.4 > /usr/lib/perl5/vendor_perl/5.8.3 > /usr/lib/perl5/vendor_perl/5.8.2 > /usr/lib/perl5/vendor_perl/5.8.1 > /usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl > > What am I doing wrong? Could you help? > > Thanks in advance for your help > Tom > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l