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From: Adhemar <az...@gm...> - 2011-06-06 15:44:59
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Hi, I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a while informing that it's not allowed to handle more than 10000 objects at one time. There's a copy of the whole output bellow. How to fix this? Thanks, Adhemar ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org ;sid=schistodb30 Mon Jun 6 12:32:15 2011 PLUGIN ApiCommonData::Load::Plugin::InsertDbESTFiles Mon Jun 6 12:32:15 2011 ARG algoinvo 1 Mon Jun 6 12:32:15 2011 ARG comment Mon Jun 6 12:32:15 2011 ARG commit 0 Mon Jun 6 12:32:15 2011 ARG debug 0 Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 Mon Jun 6 12:32:15 2011 ARG group Mon Jun 6 12:32:15 2011 ARG gusconfigfile /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config Mon Jun 6 12:32:15 2011 ARG help Mon Jun 6 12:32:15 2011 ARG helpHTML Mon Jun 6 12:32:15 2011 ARG inputFile /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est Mon Jun 6 12:32:15 2011 ARG project Mon Jun 6 12:32:15 2011 ARG restartFile Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 Mon Jun 6 12:32:15 2011 ARG user Mon Jun 6 12:32:15 2011 ARG verbose 0 Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 Mon Jun 6 12:32:15 2011 AlgInvocationId 122 Mon Jun 6 12:32:15 2011 COMMIT commit off ERROR MESSAGE: 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called **** /projects/gusApps/gus_home/bin/ga on line 11 STACK TRACE: 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)') called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 DBD::Oracle::st execute failed: ORA-12899: value too large for column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD ERROR: error possibly near <*> indicator at char 143 in ' UPDATE Core.AlgorithmInvocation SET modification_date = SYSDATE, end_time = SYSDATE, row_alg_invocation_id = :p1, result = :<*>p2 WHERE algorithm_invocation_id = :p3') [for Statement " UPDATE Core.AlgorithmInvocation SET modification_date = SYSDATE, end_time = SYSDATE, row_alg_invocation_id = ?, result = ? WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', :p2='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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)...', :p3='122'] at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <ESTs> line 149834. SQL ERROR!! involving UPDATE Core.AlgorithmInvocation SET modification_date = SYSDATE, end_time = SYSDATE, row_alg_invocation_id = ?, result = ? WHERE algorithm_invocation_id = ? Values: 122, 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called, 122 at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE Core.AlgorithmInvocatio...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET \x{a}\x{9}modificat...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 731 GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 612 GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 1681 GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 1250 GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have exceeded the maximum number of allowable objects in ...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 623 GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 |
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From: Deborah P. <pi...@pc...> - 2011-06-07 13:29:40
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This plugin is not used frequently. We use a different plugin when loading from the dbEST mirror. In the past, we used this plugin with the crypto EST file that the GA group made but have not used it recently. I have seen this error but I do not recall seeing with this plugin. I will take a look at the plugin to make sure it has an undefPointerCache and increase the number if it does. Debbie On 6/6/2011 11:44 AM, Adhemar wrote: > Hi, > I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a > while informing that it's not allowed to handle more than 10000 > objects at one time. > There's a copy of the whole output bellow. > How to fix this? > Thanks, > Adhemar > > > > ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org > <http://bagre.cebio.org>;sid=schistodb30 > Mon Jun 6 12:32:15 2011 PLUGIN > ApiCommonData::Load::Plugin::InsertDbESTFiles > Mon Jun 6 12:32:15 2011 ARG algoinvo 1 > Mon Jun 6 12:32:15 2011 ARG comment > Mon Jun 6 12:32:15 2011 ARG commit 0 > Mon Jun 6 12:32:15 2011 ARG debug 0 > Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC > Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 ARG group > Mon Jun 6 12:32:15 2011 ARG gusconfigfile > /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config > Mon Jun 6 12:32:15 2011 ARG help > Mon Jun 6 12:32:15 2011 ARG helpHTML > Mon Jun 6 12:32:15 2011 ARG inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > Mon Jun 6 12:32:15 2011 ARG project > Mon Jun 6 12:32:15 2011 ARG restartFile > Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 > Mon Jun 6 12:32:15 2011 ARG user > Mon Jun 6 12:32:15 2011 ARG verbose 0 > Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 > Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 > Mon Jun 6 12:32:15 2011 AlgInvocationId 122 > Mon Jun 6 12:32:15 2011 COMMIT commit off > > > ERROR MESSAGE: 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called > **** /projects/gusApps/gus_home/bin/ga on line 11 > > STACK TRACE: > 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 > Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded > the maximum number of allowable objects in ...', undef, > 'ARRAY(0x1c08c988)') called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > DBD::Oracle::st execute failed: ORA-12899: value too large for column > "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) > (DBD ERROR: error possibly near <*> indicator at char 143 in ' > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = :p1, > result = :<*>p2 > WHERE algorithm_invocation_id = :p3') [for Statement " > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', > :p2='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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)...', :p3='122'] at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 147, <ESTs> line 149834. > > > SQL ERROR!! involving > > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ? > Values: 122, 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called, 122 at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 166 > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE > Core.AlgorithmInvocatio...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 150 > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', > '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET > \x{a}\x{9}modificat...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 731 > > GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 612 > > GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') > called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1681 > > GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 1250 > > GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You > have exceeded the maximum number of allowable objects in ...') called > at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 623 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. > http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Rodrigo J. <jar...@gm...> - 2011-06-07 13:57:25
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I had this problem in InsertBlastSimilarities.pm and I put $self->undefPointerCache(); in a loop in insertSubjects subroutine. Bye 2011/6/7 Deborah Pinney <pi...@pc...> > This plugin is not used frequently. We use a different plugin when loading > from the dbEST mirror. In the past, we used this plugin with the crypto EST > file that the GA group made but have not used it recently. > > I have seen this error but I do not recall seeing with this plugin. > > I will take a look at the plugin to make sure it has an undefPointerCache > and increase the number if it does. > > Debbie > > > > On 6/6/2011 11:44 AM, Adhemar wrote: > > Hi, > I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a > while informing that it's not allowed to handle more than 10000 objects at > one time. > There's a copy of the whole output bellow. > How to fix this? > Thanks, > Adhemar > > > > ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org > ;sid=schistodb30 > Mon Jun 6 12:32:15 2011 PLUGIN > ApiCommonData::Load::Plugin::InsertDbESTFiles > Mon Jun 6 12:32:15 2011 ARG algoinvo 1 > Mon Jun 6 12:32:15 2011 ARG comment > Mon Jun 6 12:32:15 2011 ARG commit 0 > Mon Jun 6 12:32:15 2011 ARG debug 0 > Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC > Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 ARG group > Mon Jun 6 12:32:15 2011 ARG gusconfigfile > /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config > Mon Jun 6 12:32:15 2011 ARG help > Mon Jun 6 12:32:15 2011 ARG helpHTML > Mon Jun 6 12:32:15 2011 ARG inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > Mon Jun 6 12:32:15 2011 ARG project > Mon Jun 6 12:32:15 2011 ARG restartFile > Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 > Mon Jun 6 12:32:15 2011 ARG user > Mon Jun 6 12:32:15 2011 ARG verbose 0 > Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 > Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 > Mon Jun 6 12:32:15 2011 AlgInvocationId 122 > Mon Jun 6 12:32:15 2011 COMMIT commit off > > > ERROR MESSAGE: 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called > **** /projects/gusApps/gus_home/bin/ga on line 11 > > STACK TRACE: > 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 > Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the > maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)') > called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > DBD::Oracle::st execute failed: ORA-12899: value too large for column > "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD > ERROR: error possibly near <*> indicator at char 143 in ' > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = :p1, > result = :<*>p2 > WHERE algorithm_invocation_id = :p3') [for Statement " > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', > :p2='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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)...', :p3='122'] at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 147, <ESTs> line 149834. > > > SQL ERROR!! involving > > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ? > Values: 122, 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called, 122 at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 166 > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE > Core.AlgorithmInvocatio...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 150 > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', > '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET > \x{a}\x{9}modificat...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 731 > > GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 612 > > GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') > called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1681 > > GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 1250 > > GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have > exceeded the maximum number of allowable objects in ...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 623 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- Atc, Rodrigo Jardim jar...@gm... |
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From: Deborah P. <pi...@pc...> - 2011-06-07 14:12:54
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The plugin did not have an undefPointerCache(). I have added it. Please update from svn and set that step to ready. Debbie On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > I had this problem in InsertBlastSimilarities.pm and I put > $self->undefPointerCache(); in a loop in insertSubjects subroutine. > > Bye > > > > 2011/6/7 Deborah Pinney <pi...@pc... > <mailto:pi...@pc...>> > > This plugin is not used frequently. We use a different plugin when > loading from the dbEST mirror. In the past, we used this plugin > with the crypto EST file that the GA group made but have not used > it recently. > > I have seen this error but I do not recall seeing with this plugin. > > I will take a look at the plugin to make sure it has an > undefPointerCache and increase the number if it does. > > Debbie > > > > On 6/6/2011 11:44 AM, Adhemar wrote: >> Hi, >> I'm trying to load ESTs using InsertDbESTFiles.pm but it fails >> after a while informing that it's not allowed to handle more than >> 10000 objects at one time. >> There's a copy of the whole output bellow. >> How to fix this? >> Thanks, >> Adhemar >> >> >> >> ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile >> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >> --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 >> Mon Jun 6 12:32:15 2011 DSN >> dbi:Oracle:host=bagre.cebio.org >> <http://bagre.cebio.org>;sid=schistodb30 >> Mon Jun 6 12:32:15 2011 PLUGIN >> ApiCommonData::Load::Plugin::InsertDbESTFiles >> Mon Jun 6 12:32:15 2011 ARG algoinvo 1 >> Mon Jun 6 12:32:15 2011 ARG comment >> Mon Jun 6 12:32:15 2011 ARG commit 0 >> Mon Jun 6 12:32:15 2011 ARG debug 0 >> Mon Jun 6 12:32:15 2011 ARG extDbName >> SjapAnhui_EstLibrary_RSRC >> Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 >> Mon Jun 6 12:32:15 2011 ARG group >> Mon Jun 6 12:32:15 2011 ARG gusconfigfile >> /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config >> Mon Jun 6 12:32:15 2011 ARG help >> Mon Jun 6 12:32:15 2011 ARG helpHTML >> Mon Jun 6 12:32:15 2011 ARG inputFile >> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >> Mon Jun 6 12:32:15 2011 ARG project >> Mon Jun 6 12:32:15 2011 ARG restartFile >> Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 >> Mon Jun 6 12:32:15 2011 ARG user >> Mon Jun 6 12:32:15 2011 ARG verbose 0 >> Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 >> Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 >> Mon Jun 6 12:32:15 2011 AlgInvocationId 122 >> Mon Jun 6 12:32:15 2011 COMMIT commit off >> >> >> ERROR MESSAGE: 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 >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >> line 483 >> >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >> 'HASH(0x20a0aa20)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 336 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 212 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)', 345, 62) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 159 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d57af38)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 602 >> GUS::PluginMgr::GusApplication::__ANON__() called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >> eval {...} called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 632 >> >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 502 >> >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 388 >> >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 297 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ARRAY(0x1b7e0b48)') called >> **** /projects/gusApps/gus_home/bin/ga on line 11 >> >> STACK TRACE: >> 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 >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >> line 483 >> >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >> 'HASH(0x20a0aa20)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 336 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 212 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)', 345, 62) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 159 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d57af38)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 602 >> >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 502 >> >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 388 >> >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 297 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ARRAY(0x1b7e0b48)') called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 >> Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have >> exceeded the maximum number of allowable objects in ...', undef, >> 'ARRAY(0x1c08c988)') called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 632 >> >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 502 >> >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 388 >> >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 297 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga >> line 11 >> >> >> DBD::Oracle::st execute failed: ORA-12899: value too large for >> column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, >> maximum: 350) (DBD ERROR: error possibly near <*> indicator at >> char 143 in ' >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = :p1, >> result = :<*>p2 >> WHERE algorithm_invocation_id = :p3') [for Statement " >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = ?, >> result = ? >> WHERE algorithm_invocation_id = ?" with ParamValues: >> :p1='122', :p2='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 >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >> line 483 >> >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >> 'HASH(0x20a0aa20)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 336 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)...', :p3='122'] at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 147, <ESTs> line 149834. >> >> >> SQL ERROR!! involving >> >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = ?, >> result = ? >> WHERE algorithm_invocation_id = ? >> Values: 122, 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 >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >> line 483 >> >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >> 'HASH(0x20a0aa20)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 336 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 212 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d566110)', 345, 62) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >> line 159 >> >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'HASH(0x1d57af38)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 602 >> GUS::PluginMgr::GusApplication::__ANON__() called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >> eval {...} called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 632 >> >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 502 >> >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 388 >> >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 297 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ARRAY(0x1b7e0b48)') called, 122 at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 166 >> >> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >> '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE >> Core.AlgorithmInvocatio...') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 150 >> >> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', >> 'ARRAY(0x209b7700)', '\x{a} UPDATE >> Core.AlgorithmInvocation\x{a} SET \x{a}\x{9}modificat...') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >> line 731 >> >> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >> 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >> line 612 >> >> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 1681 >> >> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >> 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 1250 >> >> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >> 'You have exceeded the maximum number of allowable objects in >> ...') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 623 >> GUS::PluginMgr::GusApplication::__ANON__() called at >> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >> called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 632 >> >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 502 >> >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 388 >> >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 297 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga >> line 11 >> >> >> ------------------------------------------------------------------------------ >> Simplify data backup and recovery for your virtual environment with vRanger. >> Installation's a snap, and flexible recovery options mean your data is safe, >> secure and there when you need it. Discover what all the cheering's about. >> Get your free trial download today. >> http://p.sf.net/sfu/quest-dev2dev2 >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... <mailto:jar...@gm...> > > -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Adhemar <az...@gm...> - 2011-06-07 14:35:28
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We've just tested it using ga and it worked fine. Now we're adding it to the workflow. Thank you so much Debbie. -Adhemar 2011/6/7 Deborah Pinney <pi...@pc...> > The plugin did not have an undefPointerCache(). I have added it. Please > update from svn and set that step to ready. > > Debbie > > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > > I had this problem in InsertBlastSimilarities.pm and I put > $self->undefPointerCache(); in a loop in insertSubjects subroutine. > > Bye > > > > 2011/6/7 Deborah Pinney <pi...@pc...> > > This plugin is not used frequently. We use a different plugin when loading > from the dbEST mirror. In the past, we used this plugin with the crypto EST > file that the GA group made but have not used it recently. > > I have seen this error but I do not recall seeing with this plugin. > > I will take a look at the plugin to make sure it has an undefPointerCache > and increase the number if it does. > > Debbie > > > > On 6/6/2011 11:44 AM, Adhemar wrote: > > Hi, > I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a > while informing that it's not allowed to handle more than 10000 objects at > one time. > There's a copy of the whole output bellow. > How to fix this? > Thanks, > Adhemar > > > > ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org > ;sid=schistodb30 > Mon Jun 6 12:32:15 2011 PLUGIN > ApiCommonData::Load::Plugin::InsertDbESTFiles > Mon Jun 6 12:32:15 2011 ARG algoinvo 1 > Mon Jun 6 12:32:15 2011 ARG comment > Mon Jun 6 12:32:15 2011 ARG commit 0 > Mon Jun 6 12:32:15 2011 ARG debug 0 > Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC > Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 ARG group > Mon Jun 6 12:32:15 2011 ARG gusconfigfile > /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config > Mon Jun 6 12:32:15 2011 ARG help > Mon Jun 6 12:32:15 2011 ARG helpHTML > Mon Jun 6 12:32:15 2011 ARG inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > Mon Jun 6 12:32:15 2011 ARG project > Mon Jun 6 12:32:15 2011 ARG restartFile > Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 > Mon Jun 6 12:32:15 2011 ARG user > Mon Jun 6 12:32:15 2011 ARG verbose 0 > Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 > Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 > Mon Jun 6 12:32:15 2011 AlgInvocationId 122 > Mon Jun 6 12:32:15 2011 COMMIT commit off > > > ERROR MESSAGE: 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called > **** /projects/gusApps/gus_home/bin/ga on line 11 > > STACK TRACE: > 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 > Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the > maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)') > called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > DBD::Oracle::st execute failed: ORA-12899: value too large for column > "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD > ERROR: error possibly near <*> indicator at char 143 in ' > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = :p1, > result = :<*>p2 > WHERE algorithm_invocation_id = :p3') [for Statement " > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', > :p2='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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)...', :p3='122'] at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 147, <ESTs> line 149834. > > > SQL ERROR!! involving > > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ? > Values: 122, 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called, 122 at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 166 > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE > Core.AlgorithmInvocatio...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 150 > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', > '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET > \x{a}\x{9}modificat...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 731 > > GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 612 > > GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') > called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1681 > > GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 1250 > > GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have > exceeded the maximum number of allowable objects in ...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 623 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > |
|
From: Steve F. <sfi...@pc...> - 2011-06-07 14:41:08
|
adhemar, are you going to write a step class? do you know how to do that? steve On 6/7/2011 10:35 AM, Adhemar wrote: > We've just tested it using ga and it worked fine. > Now we're adding it to the workflow. > Thank you so much Debbie. > -Adhemar > > > 2011/6/7 Deborah Pinney <pi...@pc... > <mailto:pi...@pc...>> > > The plugin did not have an undefPointerCache(). I have added it. > Please update from svn and set that step to ready. > > Debbie > > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: >> I had this problem in InsertBlastSimilarities.pm and I put >> $self->undefPointerCache(); in a loop in insertSubjects subroutine. >> >> Bye >> >> >> >> 2011/6/7 Deborah Pinney <pi...@pc... >> <mailto:pi...@pc...>> >> >> This plugin is not used frequently. We use a different plugin >> when loading from the dbEST mirror. In the past, we used this >> plugin with the crypto EST file that the GA group made but >> have not used it recently. >> >> I have seen this error but I do not recall seeing with this >> plugin. >> >> I will take a look at the plugin to make sure it has an >> undefPointerCache and increase the number if it does. >> >> Debbie >> >> >> >> On 6/6/2011 11:44 AM, Adhemar wrote: >>> Hi, >>> I'm trying to load ESTs using InsertDbESTFiles.pm but it >>> fails after a while informing that it's not allowed to >>> handle more than 10000 objects at one time. >>> There's a copy of the whole output bellow. >>> How to fix this? >>> Thanks, >>> Adhemar >>> >>> >>> >>> ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile >>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>> --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 >>> Mon Jun 6 12:32:15 2011 DSN >>> dbi:Oracle:host=bagre.cebio.org >>> <http://bagre.cebio.org>;sid=schistodb30 >>> Mon Jun 6 12:32:15 2011 PLUGIN >>> ApiCommonData::Load::Plugin::InsertDbESTFiles >>> Mon Jun 6 12:32:15 2011 ARG algoinvo 1 >>> Mon Jun 6 12:32:15 2011 ARG comment >>> Mon Jun 6 12:32:15 2011 ARG commit 0 >>> Mon Jun 6 12:32:15 2011 ARG debug 0 >>> Mon Jun 6 12:32:15 2011 ARG extDbName >>> SjapAnhui_EstLibrary_RSRC >>> Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 >>> Mon Jun 6 12:32:15 2011 ARG group >>> Mon Jun 6 12:32:15 2011 ARG gusconfigfile >>> /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config >>> Mon Jun 6 12:32:15 2011 ARG help >>> Mon Jun 6 12:32:15 2011 ARG helpHTML >>> Mon Jun 6 12:32:15 2011 ARG inputFile >>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>> Mon Jun 6 12:32:15 2011 ARG project >>> Mon Jun 6 12:32:15 2011 ARG restartFile >>> Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 >>> Mon Jun 6 12:32:15 2011 ARG user >>> Mon Jun 6 12:32:15 2011 ARG verbose 0 >>> Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 >>> Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 >>> Mon Jun 6 12:32:15 2011 AlgInvocationId 122 >>> Mon Jun 6 12:32:15 2011 COMMIT commit off >>> >>> >>> ERROR MESSAGE: 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>> eval {...} called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called >>> **** /projects/gusApps/gus_home/bin/ga on line 11 >>> >>> STACK TRACE: >>> 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 >>> Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have >>> exceeded the maximum number of allowable objects in ...', >>> undef, 'ARRAY(0x1c08c988)') called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at >>> /projects/gusApps/gus_home/bin/ga line 11 >>> >>> >>> DBD::Oracle::st execute failed: ORA-12899: value too large >>> for column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: >>> 2869, maximum: 350) (DBD ERROR: error possibly near <*> >>> indicator at char 143 in ' >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = :p1, >>> result = :<*>p2 >>> WHERE algorithm_invocation_id = :p3') [for Statement " >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = ?, >>> result = ? >>> WHERE algorithm_invocation_id = ?" with ParamValues: >>> :p1='122', :p2='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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)...', :p3='122'] at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 147, <ESTs> line 149834. >>> >>> >>> SQL ERROR!! involving >>> >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = ?, >>> result = ? >>> WHERE algorithm_invocation_id = ? >>> Values: 122, 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>> eval {...} called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called, 122 at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 166 >>> >>> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>> '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE >>> Core.AlgorithmInvocatio...') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 150 >>> >>> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', >>> 'ARRAY(0x209b7700)', '\x{a} UPDATE >>> Core.AlgorithmInvocation\x{a} SET >>> \x{a}\x{9}modificat...') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>> line 731 >>> >>> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>> 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>> line 612 >>> >>> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 1681 >>> >>> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>> 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 1250 >>> >>> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'You have exceeded the maximum number of allowable objects >>> in ...') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 623 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>> at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at >>> /projects/gusApps/gus_home/bin/ga line 11 >>> >>> >>> ------------------------------------------------------------------------------ >>> Simplify data backup and recovery for your virtual environment with vRanger. >>> Installation's a snap, and flexible recovery options mean your data is safe, >>> secure and there when you need it. Discover what all the cheering's about. >>> Get your free trial download today. >>> http://p.sf.net/sfu/quest-dev2dev2 >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> -- >> Deborah Farin Pinney, Ph.D. >> Data Analyst >> 1428 Blockley Hall >> Computational Biology and Informatics Laboratory >> University of Pennsylvania >> Philadelphia PA 19104-6021 >> Tel: 215-573-3116 >> Fax: 215-573-3111 >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced >> content >> authoring tool. Experience the power of Track Changes, Inline >> Image >> Editing and ensure content is compliant with Accessibility >> Checking. >> http://p.sf.net/sfu/ephox-dev2dev >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> -- >> Atc, >> Rodrigo Jardim >> jar...@gm... <mailto:jar...@gm...> >> >> > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Deborah P. <pi...@pc...> - 2011-06-07 14:41:19
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Did your previous run actually load any rows? You can check by querying the dots.est table with row_alg_invocation_id = 122. If there are any rows, they will have to be deleted, otherwise you will have duplicate rows. Since use of this plugin has been discontinued in the EuPath group, we have not yet added an undo subroutine. I will add that now and resubmit to svn. Debbie On 6/7/2011 10:12 AM, Deborah Pinney wrote: > The plugin did not have an undefPointerCache(). I have added it. > Please update from svn and set that step to ready. > > Debbie > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: >> I had this problem in InsertBlastSimilarities.pm and I put >> $self->undefPointerCache(); in a loop in insertSubjects subroutine. >> >> Bye >> >> >> >> 2011/6/7 Deborah Pinney <pi...@pc... >> <mailto:pi...@pc...>> >> >> This plugin is not used frequently. We use a different plugin >> when loading from the dbEST mirror. In the past, we used this >> plugin with the crypto EST file that the GA group made but have >> not used it recently. >> >> I have seen this error but I do not recall seeing with this plugin. >> >> I will take a look at the plugin to make sure it has an >> undefPointerCache and increase the number if it does. >> >> Debbie >> >> >> >> On 6/6/2011 11:44 AM, Adhemar wrote: >>> Hi, >>> I'm trying to load ESTs using InsertDbESTFiles.pm but it fails >>> after a while informing that it's not allowed to handle more >>> than 10000 objects at one time. >>> There's a copy of the whole output bellow. >>> How to fix this? >>> Thanks, >>> Adhemar >>> >>> >>> >>> ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile >>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>> --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 >>> Mon Jun 6 12:32:15 2011 DSN >>> dbi:Oracle:host=bagre.cebio.org >>> <http://bagre.cebio.org>;sid=schistodb30 >>> Mon Jun 6 12:32:15 2011 PLUGIN >>> ApiCommonData::Load::Plugin::InsertDbESTFiles >>> Mon Jun 6 12:32:15 2011 ARG algoinvo 1 >>> Mon Jun 6 12:32:15 2011 ARG comment >>> Mon Jun 6 12:32:15 2011 ARG commit 0 >>> Mon Jun 6 12:32:15 2011 ARG debug 0 >>> Mon Jun 6 12:32:15 2011 ARG extDbName >>> SjapAnhui_EstLibrary_RSRC >>> Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 >>> Mon Jun 6 12:32:15 2011 ARG group >>> Mon Jun 6 12:32:15 2011 ARG gusconfigfile >>> /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config >>> Mon Jun 6 12:32:15 2011 ARG help >>> Mon Jun 6 12:32:15 2011 ARG helpHTML >>> Mon Jun 6 12:32:15 2011 ARG inputFile >>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>> Mon Jun 6 12:32:15 2011 ARG project >>> Mon Jun 6 12:32:15 2011 ARG restartFile >>> Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 >>> Mon Jun 6 12:32:15 2011 ARG user >>> Mon Jun 6 12:32:15 2011 ARG verbose 0 >>> Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 >>> Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 >>> Mon Jun 6 12:32:15 2011 AlgInvocationId 122 >>> Mon Jun 6 12:32:15 2011 COMMIT commit off >>> >>> >>> ERROR MESSAGE: 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>> eval {...} called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called >>> **** /projects/gusApps/gus_home/bin/ga on line 11 >>> >>> STACK TRACE: >>> 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 >>> Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have >>> exceeded the maximum number of allowable objects in ...', undef, >>> 'ARRAY(0x1c08c988)') called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga >>> line 11 >>> >>> >>> DBD::Oracle::st execute failed: ORA-12899: value too large for >>> column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, >>> maximum: 350) (DBD ERROR: error possibly near <*> indicator at >>> char 143 in ' >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = :p1, >>> result = :<*>p2 >>> WHERE algorithm_invocation_id = :p3') [for Statement " >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = ?, >>> result = ? >>> WHERE algorithm_invocation_id = ?" with ParamValues: >>> :p1='122', :p2='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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)...', :p3='122'] at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 147, <ESTs> line 149834. >>> >>> >>> SQL ERROR!! involving >>> >>> UPDATE Core.AlgorithmInvocation >>> SET >>> modification_date = SYSDATE, >>> end_time = SYSDATE, >>> row_alg_invocation_id = ?, >>> result = ? >>> WHERE algorithm_invocation_id = ? >>> Values: 122, 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 >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>> line 483 >>> >>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 28 >>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>> 'HASH(0x20a0aa20)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 336 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 212 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d566110)', 345, 62) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>> line 159 >>> >>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>> 'HASH(0x1d57af38)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 602 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>> eval {...} called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called, 122 at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 166 >>> >>> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>> '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE >>> Core.AlgorithmInvocatio...') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 150 >>> >>> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', >>> 'ARRAY(0x209b7700)', '\x{a} UPDATE >>> Core.AlgorithmInvocation\x{a} SET >>> \x{a}\x{9}modificat...') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>> line 731 >>> >>> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>> 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>> line 612 >>> >>> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>> line 1681 >>> >>> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>> 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 1250 >>> >>> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You >>> have exceeded the maximum number of allowable objects in ...') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 623 >>> GUS::PluginMgr::GusApplication::__ANON__() called at >>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 >>> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') >>> called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 632 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 502 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 388 >>> >>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>> line 297 >>> >>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga >>> line 11 >>> >>> >>> ------------------------------------------------------------------------------ >>> Simplify data backup and recovery for your virtual environment with vRanger. >>> Installation's a snap, and flexible recovery options mean your data is safe, >>> secure and there when you need it. Discover what all the cheering's about. >>> Get your free trial download today. >>> http://p.sf.net/sfu/quest-dev2dev2 >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> -- >> Deborah Farin Pinney, Ph.D. >> Data Analyst >> 1428 Blockley Hall >> Computational Biology and Informatics Laboratory >> University of Pennsylvania >> Philadelphia PA 19104-6021 >> Tel: 215-573-3116 >> Fax: 215-573-3111 >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced content >> authoring tool. Experience the power of Track Changes, Inline Image >> Editing and ensure content is compliant with Accessibility Checking. >> http://p.sf.net/sfu/ephox-dev2dev >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> -- >> Atc, >> Rodrigo Jardim >> jar...@gm... <mailto:jar...@gm...> >> >> > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Adhemar <az...@gm...> - 2011-06-07 15:12:29
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I've ran it using commit OFF so that nothing is actually inserted into the database. We chose this plugin because it loads not only the EST sequence but also the libraries, contacts, and references. If it eventually breaks we can use GUS::Community::Plugin::Undo. But it would be nice to have the undo subroutine. Thanks, -Adhemar 2011/6/7 Deborah Pinney <pi...@pc...> > Did your previous run actually load any rows? You can check by querying > the dots.est table with row_alg_invocation_id = 122. If there are any rows, > they will have to be deleted, otherwise you will have duplicate rows. Since > use of this plugin has been discontinued in the EuPath group, we have not > yet added an undo subroutine. I will add that now and resubmit to svn. > > Debbie > > > On 6/7/2011 10:12 AM, Deborah Pinney wrote: > > The plugin did not have an undefPointerCache(). I have added it. Please > update from svn and set that step to ready. > > Debbie > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > > I had this problem in InsertBlastSimilarities.pm and I put > $self->undefPointerCache(); in a loop in insertSubjects subroutine. > > Bye > > > > 2011/6/7 Deborah Pinney <pi...@pc...> > > This plugin is not used frequently. We use a different plugin when loading > from the dbEST mirror. In the past, we used this plugin with the crypto EST > file that the GA group made but have not used it recently. > > I have seen this error but I do not recall seeing with this plugin. > > I will take a look at the plugin to make sure it has an undefPointerCache > and increase the number if it does. > > Debbie > > > > On 6/6/2011 11:44 AM, Adhemar wrote: > > Hi, > I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a > while informing that it's not allowed to handle more than 10000 objects at > one time. > There's a copy of the whole output bellow. > How to fix this? > Thanks, > Adhemar > > > > ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org > ;sid=schistodb30 > Mon Jun 6 12:32:15 2011 PLUGIN > ApiCommonData::Load::Plugin::InsertDbESTFiles > Mon Jun 6 12:32:15 2011 ARG algoinvo 1 > Mon Jun 6 12:32:15 2011 ARG comment > Mon Jun 6 12:32:15 2011 ARG commit 0 > Mon Jun 6 12:32:15 2011 ARG debug 0 > Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC > Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 > Mon Jun 6 12:32:15 2011 ARG group > Mon Jun 6 12:32:15 2011 ARG gusconfigfile > /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config > Mon Jun 6 12:32:15 2011 ARG help > Mon Jun 6 12:32:15 2011 ARG helpHTML > Mon Jun 6 12:32:15 2011 ARG inputFile > /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est > Mon Jun 6 12:32:15 2011 ARG project > Mon Jun 6 12:32:15 2011 ARG restartFile > Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 > Mon Jun 6 12:32:15 2011 ARG user > Mon Jun 6 12:32:15 2011 ARG verbose 0 > Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 > Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 > Mon Jun 6 12:32:15 2011 AlgInvocationId 122 > Mon Jun 6 12:32:15 2011 COMMIT commit off > > > ERROR MESSAGE: 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called > **** /projects/gusApps/gus_home/bin/ga on line 11 > > STACK TRACE: > 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 > Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the > maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)') > called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > DBD::Oracle::st execute failed: ORA-12899: value too large for column > "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD > ERROR: error possibly near <*> indicator at char 143 in ' > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = :p1, > result = :<*>p2 > WHERE algorithm_invocation_id = :p3') [for Statement " > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', > :p2='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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)...', :p3='122'] at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 147, <ESTs> line 149834. > > > SQL ERROR!! involving > > UPDATE Core.AlgorithmInvocation > SET > modification_date = SYSDATE, > end_time = SYSDATE, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ? > Values: 122, 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 > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm > line 483 > > GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', > 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 28 > GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', > 'HASH(0x20a0aa20)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 336 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 212 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d566110)', 345, 62) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm > line 159 > > ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', > 'HASH(0x1d57af38)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 602 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 > eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm > line 407 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called, 122 at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 166 > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE > Core.AlgorithmInvocatio...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 150 > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', > '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET > \x{a}\x{9}modificat...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 731 > > GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 612 > > GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') > called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1681 > > GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', > 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 1250 > > GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have > exceeded the maximum number of allowable objects in ...') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 623 > GUS::PluginMgr::GusApplication::__ANON__() called at > /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 > Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 632 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 502 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 388 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at > /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 297 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', > 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking.http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Deborah P. <pi...@pc...> - 2011-06-07 15:27:47
|
The plugin has to have the undoTables subroutine to allow Undo.pm to work. Unfortunately I was almost done adding the subroutine when we lost connectivity. I will do that now and commit to svn. Debbie On 6/7/2011 11:12 AM, Adhemar wrote: > I've ran it using commit OFF so that nothing is actually inserted into > the database. > We chose this plugin because it loads not only the EST sequence but > also the libraries, contacts, and references. > If it eventually breaks we can use GUS::Community::Plugin::Undo. > But it would be nice to have the undo subroutine. > Thanks, > -Adhemar > > > 2011/6/7 Deborah Pinney <pi...@pc... > <mailto:pi...@pc...>> > > Did your previous run actually load any rows? You can check by > querying the dots.est table with row_alg_invocation_id = 122. If > there are any rows, they will have to be deleted, otherwise you > will have duplicate rows. Since use of this plugin has been > discontinued in the EuPath group, we have not yet added an undo > subroutine. I will add that now and resubmit to svn. > > Debbie > > > On 6/7/2011 10:12 AM, Deborah Pinney wrote: >> The plugin did not have an undefPointerCache(). I have added it. >> Please update from svn and set that step to ready. >> >> Debbie >> >> On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: >>> I had this problem in InsertBlastSimilarities.pm and I put >>> $self->undefPointerCache(); in a loop in insertSubjects subroutine. >>> >>> Bye >>> >>> >>> >>> 2011/6/7 Deborah Pinney <pi...@pc... >>> <mailto:pi...@pc...>> >>> >>> This plugin is not used frequently. We use a different >>> plugin when loading from the dbEST mirror. In the past, we >>> used this plugin with the crypto EST file that the GA group >>> made but have not used it recently. >>> >>> I have seen this error but I do not recall seeing with this >>> plugin. >>> >>> I will take a look at the plugin to make sure it has an >>> undefPointerCache and increase the number if it does. >>> >>> Debbie >>> >>> >>> >>> On 6/6/2011 11:44 AM, Adhemar wrote: >>>> Hi, >>>> I'm trying to load ESTs using InsertDbESTFiles.pm but it >>>> fails after a while informing that it's not allowed to >>>> handle more than 10000 objects at one time. >>>> There's a copy of the whole output bellow. >>>> How to fix this? >>>> Thanks, >>>> Adhemar >>>> >>>> >>>> >>>> ga ApiCommonData::Load::Plugin::InsertDbESTFiles >>>> --inputFile >>>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>>> --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 >>>> Mon Jun 6 12:32:15 2011 DSN >>>> dbi:Oracle:host=bagre.cebio.org >>>> <http://bagre.cebio.org>;sid=schistodb30 >>>> Mon Jun 6 12:32:15 2011 PLUGIN >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles >>>> Mon Jun 6 12:32:15 2011 ARG algoinvo 1 >>>> Mon Jun 6 12:32:15 2011 ARG comment >>>> Mon Jun 6 12:32:15 2011 ARG commit 0 >>>> Mon Jun 6 12:32:15 2011 ARG debug 0 >>>> Mon Jun 6 12:32:15 2011 ARG extDbName >>>> SjapAnhui_EstLibrary_RSRC >>>> Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 >>>> Mon Jun 6 12:32:15 2011 ARG group >>>> Mon Jun 6 12:32:15 2011 ARG gusconfigfile >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config >>>> Mon Jun 6 12:32:15 2011 ARG help >>>> Mon Jun 6 12:32:15 2011 ARG helpHTML >>>> Mon Jun 6 12:32:15 2011 ARG inputFile >>>> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >>>> Mon Jun 6 12:32:15 2011 ARG project >>>> Mon Jun 6 12:32:15 2011 ARG restartFile >>>> Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 >>>> Mon Jun 6 12:32:15 2011 ARG user >>>> Mon Jun 6 12:32:15 2011 ARG verbose 0 >>>> Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 >>>> Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 >>>> Mon Jun 6 12:32:15 2011 AlgInvocationId 122 >>>> Mon Jun 6 12:32:15 2011 COMMIT commit off >>>> >>>> >>>> ERROR MESSAGE: 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 >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>>> line 483 >>>> >>>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>>> line 28 >>>> >>>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>>> 'HASH(0x20a0aa20)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 336 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 212 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)', 345, 62) called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 159 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d57af38)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 602 >>>> GUS::PluginMgr::GusApplication::__ANON__() called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>>> eval {...} called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>>> Error::subs::try('CODE(0x1d39cdf8)', >>>> 'HASH(0x1d57b5c8)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 632 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 502 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 388 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 297 >>>> >>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ARRAY(0x1b7e0b48)') called >>>> **** /projects/gusApps/gus_home/bin/ga on line 11 >>>> >>>> STACK TRACE: >>>> 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 >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>>> line 483 >>>> >>>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>>> line 28 >>>> >>>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>>> 'HASH(0x20a0aa20)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 336 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 212 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)', 345, 62) called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 159 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d57af38)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 602 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 502 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 388 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 297 >>>> >>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ARRAY(0x1b7e0b48)') called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 >>>> Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have >>>> exceeded the maximum number of allowable objects in ...', >>>> undef, 'ARRAY(0x1c08c988)') called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 >>>> Error::subs::try('CODE(0x1d39cdf8)', >>>> 'HASH(0x1d57b5c8)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 632 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 502 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 388 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 297 >>>> >>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ARRAY(0x1b7e0b48)') called at >>>> /projects/gusApps/gus_home/bin/ga line 11 >>>> >>>> >>>> DBD::Oracle::st execute failed: ORA-12899: value too large >>>> for column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: >>>> 2869, maximum: 350) (DBD ERROR: error possibly near <*> >>>> indicator at char 143 in ' >>>> UPDATE Core.AlgorithmInvocation >>>> SET >>>> modification_date = SYSDATE, >>>> end_time = SYSDATE, >>>> row_alg_invocation_id = :p1, >>>> result = :<*>p2 >>>> WHERE algorithm_invocation_id = :p3') [for Statement " >>>> UPDATE Core.AlgorithmInvocation >>>> SET >>>> modification_date = SYSDATE, >>>> end_time = SYSDATE, >>>> row_alg_invocation_id = ?, >>>> result = ? >>>> WHERE algorithm_invocation_id = ?" with ParamValues: >>>> :p1='122', :p2='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 >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>>> line 483 >>>> >>>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>>> line 28 >>>> >>>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>>> 'HASH(0x20a0aa20)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 336 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)...', :p3='122'] at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>>> line 147, <ESTs> line 149834. >>>> >>>> >>>> SQL ERROR!! involving >>>> >>>> UPDATE Core.AlgorithmInvocation >>>> SET >>>> modification_date = SYSDATE, >>>> end_time = SYSDATE, >>>> row_alg_invocation_id = ?, >>>> result = ? >>>> WHERE algorithm_invocation_id = ? >>>> Values: 122, 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 >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm >>>> line 483 >>>> >>>> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', >>>> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>>> line 28 >>>> >>>> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', >>>> 'HASH(0x20a0aa20)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 336 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 212 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d566110)', 345, 62) called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm >>>> line 159 >>>> >>>> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'HASH(0x1d57af38)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 602 >>>> GUS::PluginMgr::GusApplication::__ANON__() called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >>>> eval {...} called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >>>> Error::subs::try('CODE(0x1d39cdf8)', >>>> 'HASH(0x1d57b5c8)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 632 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 502 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 388 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 297 >>>> >>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ARRAY(0x1b7e0b48)') called, 122 at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>>> line 166 >>>> >>>> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>>> '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE >>>> Core.AlgorithmInvocatio...') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>>> line 150 >>>> >>>> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', >>>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', >>>> 'ARRAY(0x209b7700)', '\x{a} UPDATE >>>> Core.AlgorithmInvocation\x{a} SET >>>> \x{a}\x{9}modificat...') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>>> line 731 >>>> >>>> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>>> 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>>> line 612 >>>> >>>> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') >>>> called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm >>>> line 1681 >>>> >>>> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', >>>> 1) called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 1250 >>>> >>>> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', >>>> 'You have exceeded the maximum number of allowable objects >>>> in ...') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 623 >>>> GUS::PluginMgr::GusApplication::__ANON__() called at >>>> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 >>>> Error::subs::try('CODE(0x1d39cdf8)', >>>> 'HASH(0x1d57b5c8)') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 632 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called >>>> at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 502 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 388 >>>> >>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at >>>> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >>>> line 297 >>>> >>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', >>>> 'ARRAY(0x1b7e0b48)') called at >>>> /projects/gusApps/gus_home/bin/ga line 11 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Simplify data backup and recovery for your virtual environment with vRanger. >>>> Installation's a snap, and flexible recovery options mean your data is safe, >>>> secure and there when you need it. Discover what all the cheering's about. >>>> Get your free trial download today. >>>> http://p.sf.net/sfu/quest-dev2dev2 >>>> >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... <mailto:Gus...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> -- >>> Deborah Farin Pinney, Ph.D. >>> Data Analyst >>> 1428 Blockley Hall >>> Computational Biology and Informatics Laboratory >>> University of Pennsylvania >>> Philadelphia PA 19104-6021 >>> Tel: 215-573-3116 >>> Fax: 215-573-3111 >>> >>> >>> ------------------------------------------------------------------------------ >>> EditLive Enterprise is the world's most technically advanced >>> content >>> authoring tool. Experience the power of Track Changes, >>> Inline Image >>> Editing and ensure content is compliant with Accessibility >>> Checking. >>> http://p.sf.net/sfu/ephox-dev2dev >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> >>> -- >>> Atc, >>> Rodrigo Jardim >>> jar...@gm... <mailto:jar...@gm...> >>> >>> >> >> -- >> Deborah Farin Pinney, Ph.D. >> Data Analyst >> 1428 Blockley Hall >> Computational Biology and Informatics Laboratory >> University of Pennsylvania >> Philadelphia PA 19104-6021 >> Tel: 215-573-3116 >> Fax: 215-573-3111 >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced content >> authoring tool. Experience the power of Track Changes, Inline Image >> Editing and ensure content is compliant with Accessibility Checking. >> http://p.sf.net/sfu/ephox-dev2dev >> >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Brian B. <br...@pc...> - 2011-06-07 15:24:17
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Rodrigo, you have to be very careful about where you put this method as it makes all object relationships unreachable so unless you have them in a data structure, they are effectively gone and can thus be garbage collected. Should be added to an outer loop typically after a submit call for a logical set of data. Without looking at the code, it sounds dangerous to me to have it in the insertSubjects subroutine .. I would expect it to be at a higher level and call it once for each query sequence. -Brian On Jun 7, 2011, at 9:57 AM, Rodrigo Jardim wrote: > I had this problem in InsertBlastSimilarities.pm and I put $self->undefPointerCache(); in a loop in insertSubjects subroutine. > > Bye > > > > 2011/6/7 Deborah Pinney <pi...@pc...> > This plugin is not used frequently. We use a different plugin when loading from the dbEST mirror. In the past, we used this plugin with the crypto EST file that the GA group made but have not used it recently. > > I have seen this error but I do not recall seeing with this plugin. > > I will take a look at the plugin to make sure it has an undefPointerCache and increase the number if it does. > > Debbie > > > > On 6/6/2011 11:44 AM, Adhemar wrote: >> Hi, >> I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a while informing that it's not allowed to handle more than 10000 objects at one time. >> There's a copy of the whole output bellow. >> How to fix this? >> Thanks, >> Adhemar >> >> >> >> ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03 >> Mon Jun 6 12:32:15 2011 DSN dbi:Oracle:host=bagre.cebio.org;sid=schistodb30 >> Mon Jun 6 12:32:15 2011 PLUGIN ApiCommonData::Load::Plugin::InsertDbESTFiles >> Mon Jun 6 12:32:15 2011 ARG algoinvo 1 >> Mon Jun 6 12:32:15 2011 ARG comment >> Mon Jun 6 12:32:15 2011 ARG commit 0 >> Mon Jun 6 12:32:15 2011 ARG debug 0 >> Mon Jun 6 12:32:15 2011 ARG extDbName SjapAnhui_EstLibrary_RSRC >> Mon Jun 6 12:32:15 2011 ARG extDbRlsVer 2011-06-03 >> Mon Jun 6 12:32:15 2011 ARG group >> Mon Jun 6 12:32:15 2011 ARG gusconfigfile /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config >> Mon Jun 6 12:32:15 2011 ARG help >> Mon Jun 6 12:32:15 2011 ARG helpHTML >> Mon Jun 6 12:32:15 2011 ARG inputFile /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est >> Mon Jun 6 12:32:15 2011 ARG project >> Mon Jun 6 12:32:15 2011 ARG restartFile >> Mon Jun 6 12:32:15 2011 ARG sqlVerbose 0 >> Mon Jun 6 12:32:15 2011 ARG user >> Mon Jun 6 12:32:15 2011 ARG verbose 0 >> Mon Jun 6 12:32:15 2011 ARG veryVerbose 0 >> Mon Jun 6 12:32:15 2011 ARG workflowstepid 0 >> Mon Jun 6 12:32:15 2011 AlgInvocationId 122 >> Mon Jun 6 12:32:15 2011 COMMIT commit off >> >> >> ERROR MESSAGE: 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 >> GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >> eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called >> **** /projects/gusApps/gus_home/bin/ga on line 11 >> >> STACK TRACE: >> 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306 >> Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)') called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 >> >> >> DBD::Oracle::st execute failed: ORA-12899: value too large for column "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD ERROR: error possibly near <*> indicator at char 143 in ' >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = :p1, >> result = :<*>p2 >> WHERE algorithm_invocation_id = :p3') [for Statement " >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = ?, >> result = ? >> WHERE algorithm_invocation_id = ?" with ParamValues: :p1='122', :p2='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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)...', :p3='122'] at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <ESTs> line 149834. >> >> >> SQL ERROR!! involving >> >> UPDATE Core.AlgorithmInvocation >> SET >> modification_date = SYSDATE, >> end_time = SYSDATE, >> row_alg_invocation_id = ?, >> result = ? >> WHERE algorithm_invocation_id = ? >> Values: 122, 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 /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483 >> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)', 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 >> GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef', 'HASH(0x20a0aa20)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 336 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 212 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d566110)', 345, 62) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm line 159 >> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'HASH(0x1d57af38)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 602 >> GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415 >> eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 407 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called, 122 at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 >> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', '\x{a} SQL ERROR!! involving\x{a} \x{a} UPDATE Core.AlgorithmInvocatio...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 >> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)', '\x{a} UPDATE Core.AlgorithmInvocation\x{a} SET \x{a}\x{9}modificat...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 731 >> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 612 >> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm line 1681 >> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 1250 >> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have exceeded the maximum number of allowable objects in ...') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 623 >> GUS::PluginMgr::GusApplication::__ANON__() called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429 >> Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 632 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 502 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 388 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 297 >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)', 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11 >> >> >> ------------------------------------------------------------------------------ >> Simplify data backup and recovery for your virtual environment with vRanger. >> Installation's a snap, and flexible recovery options mean your data is safe, >> secure and there when you need it. Discover what all the cheering's about. >> Get your free trial download today. >> http://p.sf.net/sfu/quest-dev2dev2 >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev Brian P. Brunk, Ph.D. EuPathDB Manager 1403 Blockley Hall Penn Center For Bioinformatics University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3118 Fax: 215-573-3111 |
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