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From: <hen...@gm...> - 2005-10-26 18:20:45
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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.proper=
ties
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::DbiData=
base=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb469c8=
4)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HASH(=
0x96a2b08)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOnt=
ology.pm
line 159
GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOntolog=
y('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','GO:00=
50834','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/InsertSequenceOntology.p=
m
line 137
GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Supported=
::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::Plugi=
nMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequ=
enceOntology',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnto=
logy')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOntology=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=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::DbiData=
base=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb469c8=
4)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HASH(=
0x96a2b08)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOnt=
ology.pm
line 159
GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOntolog=
y('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','GO:00=
50834','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/InsertSequenceOntology.p=
m
line 137
GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Supported=
::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::Plugi=
nMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequ=
enceOntology',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnto=
logy')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOntology=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=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 fellows,
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)
|
|
From: Steve F. <sfi...@pc...> - 2005-10-26 21:05:25
|
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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> =20
>
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