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Re: [GUSDEV] ISO error
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From: Steve F. <sfi...@pc...> - 2005-10-26 21:05:25
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henrique-
i am confused. no, GO.defs does not sound like the right file. where=20
did you get it? that sounds like Gene Ontology not Sequence Ontology.
steve
Henrique Juc=E1 wrote:
>Hi Michael,
>
>Thanks for the attention. Steve's suggestion solved my problem. Sorry
>about that resumed error I printed, I'll paste the whole message next
>time. Now, I'm facing a problem w/ InsertSequenceOntology. We're
>using Postgres here, and when I tried to upload GO.defs (is that the
>right file? - i checked so.definitions and it seems to have just
>changed its name), and I received this message:
>
>[juca1@kineto3 GUS]$ ga GUS::Supported::Plugin::InsertSequenceOntology
>--inputFile /gus/GUS-Files/GO/GO.defs --soCvsVersion '1.419'
>--soVersion '3.3.48' --user juca --group TESTE --commit
>Wed Oct 26 15:01:05 2005 ARGS algoinvo 1
>Wed Oct 26 15:01:05 2005 ARGS comment
>Wed Oct 26 15:01:05 2005 ARGS commit 1
>Wed Oct 26 15:01:05 2005 ARGS debug 0
>Wed Oct 26 15:01:05 2005 ARGS group TESTE
>Wed Oct 26 15:01:05 2005 ARGS gusconfigfile /gus/GUS/gus.pro=
perties
>Wed Oct 26 15:01:05 2005 ARGS help
>Wed Oct 26 15:01:05 2005 ARGS helpHTML
>Wed Oct 26 15:01:05 2005 ARGS inputFile =20
>/gus/GUS-Files/GO/GO.defs
>Wed Oct 26 15:01:05 2005 ARGS project
>Wed Oct 26 15:01:05 2005 ARGS soCvsVersion 1.419
>Wed Oct 26 15:01:05 2005 ARGS soVersion 3.3.48
>Wed Oct 26 15:01:05 2005 ARGS sqlVerbose 0
>Wed Oct 26 15:01:05 2005 ARGS user juca
>Wed Oct 26 15:01:05 2005 ARGS verbose 0
>Wed Oct 26 15:01:05 2005 ARGS veryVerbose 0
>Wed Oct 26 15:01:05 2005 COMMIT commit on
>Wed Oct 26 15:01:05 2005 ALGINVID 10
>
>ERROR:
>You have exceeded the maximum number of allowable objects in memory:
> You must use the method 'undefPointerCache()' in each loop
> to clear the cache and allow garbage collection!!
> If you need > 10000 objects at one time,
> then increase the default number with the method
>'setMaximumNumberOfObjects(<number>)' at
>/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiD=
atabase=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb=
469c84)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
> GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HA=
SH(0x96a2b08)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence=
Ontology.pm
>line 159
> GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOnto=
logy('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','=
GO:0050834','molybdenum
>incorporation via L-cysteinyl copper sulfido molyb...','The
>incorporation of molybdenum into a protein by L-cysteinyl...') called
>at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntolog=
y.pm
>line 137
> GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Suppor=
ted::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
> eval {...} called at
>/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::Inser=
tSequenceOntology',1)
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenc=
eOntology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnt=
ology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
>called at /gus/GUS/gus_home/bin/ga line 11
>
>STACK TRACE:
> at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiD=
atabase=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb=
469c84)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
> GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HA=
SH(0x96a2b08)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence=
Ontology.pm
>line 159
> GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOnto=
logy('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','=
GO:0050834','molybdenum
>incorporation via L-cysteinyl copper sulfido molyb...','The
>incorporation of molybdenum into a protein by L-cysteinyl...') called
>at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntolog=
y.pm
>line 137
> GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Suppor=
ted::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
> eval {...} called at
>/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::Inser=
tSequenceOntology',1)
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenc=
eOntology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnt=
ology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
>called at /gus/GUS/gus_home/bin/ga line 11
>
>
>Thanks for the time,
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
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