From: Shane M. <sha...@gm...> - 2016-10-26 22:01:35
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You were right - I accidentally removed the new Adapter.pm. Thanks! Running the script is throwing another error though. It did show the 'unable to find synonym type' error for all 200,000+ lines of this sample gff. I uploaded the ontologies/schema from Eric here <https://github.com/erasche/chado-schema-builder/releases>, 1.31-jenkins93 / chado-1.31.sql.gz. unable to find synonym type in cvterm table at > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> line > 202429. > unable to find synonym type in cvterm table at > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 3088, <GEN0> line > 202430. > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: I couldn't find the 'Note' cvterm in the database; > Did you load the feature property controlled vocabulary? > STACK: Error::throw > STACK: Bio::Root::Root::throw > /home/bjreadin/src/bioperl-live/Bio/Root/Root.pm:444 > STACK: Bio::GMOD::DB::Adapter::handle_note > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm:3901 > STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:974 > ----------------------------------------------------------- > Abnormal termination, trying to clean up... > Attempting to clean up the loader temp table (so that --recreate_cache > won't be needed)... > Trying to remove the run lock (so that --remove_lock won't be needed)... > Exiting... I just ran this and wanted to share - I'll look into the other errors too. Thanks! On Wed, Oct 26, 2016 at 5:39 PM, Scott Cain <sc...@sc...> wrote: > (re cc-ing the schema mailing list) > > Hi Shane, > > I think you must not have put the new version of Adapter.pm in > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/ because line 498 of that module > doesn't mention shift, it's: > > my $arg = shift; > > Can you double check that file? > > Scott > > > > On Wed, Oct 26, 2016 at 5:22 PM, Shane McCoy <sha...@gm...> > wrote: > > > > Hi Scott! > > Thanks for the information. > > I did replace the Adapter.pm file and did a clean restart of chado and > still got the error: > >> > >> $ gmod_bulk_load_gff3.pl --noexon --analysis --organism Stripedbass > --gfffile SBDraft_Pt5.nodna.gff --dbname apollo-db > >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) > at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498. > >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl > line 13. > >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_ > gff3.pl line 13. > > > > > > Should I setup an earlier version Perl maybe? I used v5.18.2 previously > on another server and did not have this issue. > > Thanks! > > Shane M. > > > > On Wed, Oct 26, 2016 at 11:34 AM, Scott Cain <sc...@sc...> > wrote: > >> > >> Hi Shane, > >> > >> The loader module, lib/Bio/GMOD/DB/Adaptor.pm, is quite old and uses an > ugly idiom that I'd rather not talk about but it's use has be deprecated in > modern Perl. I don't have a working instance of Chado I can test with > handy (later in the week I could spin something up on AWS, but I don't have > time now), but I did commit this to github if you want to try it out: > >> > >> https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_ > defined/chado/lib/Bio/GMOD/DB/Adapter.pm > >> > >> Just download this and replace the one it's complaining about in > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm. > >> > >> Also, you won't be able to load the Relations Ontology via the make > command. You'll need to download > >> > >> http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo > >> > >> and use the commands described in INSTALL.Chado. In brief: > >> > >> $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ > >> go-apply-xslt oboxml_to_chadoxml - > obo_text.xml > >> > >> and > >> > >> $ stag-storenode.pl \ > >> -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' > \ > >> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml > >> > >> Depending on how you installed DBIx::DBStag, the ".pl" on > stag-storenode.pl might have to be removed. > >> > >> Good luck! > >> Scott > >> > >> > >> On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm...> > wrote: > >> > > >> > > >> > Hello, > >> > Using Chado VERSION=1.31 > >> > I am getting this error when using the gmod bulk load for Chado: > >> > > >> >> $ gmod_bulk_load_gff3.pl --noexon --analysis --organism > "stripedbass" --gfffile SBDraft_Full.nodna.gff --dbname apollo-db > >> >> Can't use 'defined(@array)' (Maybe you should just omit the > defined()?) at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line > 498. > >> >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_ > gff3.pl line 13. > >> >> BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_ > gff3.pl line 13. > >> > > >> > > >> > I have bioperl 1.006925 installed. I did see that the make ontologies > fails now, > >> >> > >> >> Which ontologies would you like to load (Comma delimited)? [0] > 1,2,3,4 > >> >> fetching files for Relationship Ontology > >> >> +http://www.obofoundry.org/ro/ro.obo > >> >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo) > >> >> fetching files for Sequence Ontology > >> > > >> > > >> > I am using the https://cpt.tamu.edu/computer- > resources/chado-prebuilt-schema/ recommended sql for this build. > >> > > >> > Any thoughts why this is failing? Thanks! > >> > Shane M. > >> > > >> > > >> > > >> > > >> > ------------------------------------------------------------ > ------------------ > >> > The Command Line: Reinvented for Modern Developers > >> > Did the resurgence of CLI tooling catch you by surprise? > >> > Reconnect with the command line and become more productive. > >> > Learn the new .NET and ASP.NET CLI. Get your free copy! > >> > http://sdm.link/telerik > >> > _______________________________________________ > >> > Gmod-schema mailing list > >> > Gmo...@li... > >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema > >> > > >> > >> > >> > >> -- > >> ------------------------------------------------------------ > ------------ > >> Scott Cain, Ph. D. scott at scottcain > dot net > >> GMOD Coordinator (http://gmod.org/) 216-392-3087 > >> Ontario Institute for Cancer Research > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > |