From: Ricardo B. <rb...@gm...> - 2006-01-26 16:54:02
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Hi all, After making some changes in the gus mapping file to ignore some features of the kinetoplastida database, I followed in the execution of the ISF, however without success. Somebody could help me with this error? thanks in advance, Ricardo ERROR: ------------- EXCEPTION ------------- MSG: structure_type 2 is currently unknown STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/bioperl15/Bio/SeqFeature/Tools/Unflattener.pm:1419 STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:353 STACK GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:720 STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:330 STACK (eval) /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:549 STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:541 STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:459 STACK GUS::PluginMgr::GusApplication::doMajorMode /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:357 STACK GUS::PluginMgr::GusApplication::parseAndRun /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:266 STACK toplevel /GUS/gus_home/bin/ga:11 -------------------------------------- STACK TRACE: at /usr/local/bioperl15/Bio/Root/Root.pm line 342 Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=3DHASH(0xb5e124= c)', 'structure_type 2 is currently unknown') called at /usr/local/bioperl15/Bio/SeqFeature/Tools/Unflattener.pm line 1419 Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Tools:= :Unflattener=3DHASH(0xb5e124c)', '-seq', 'Bio::Seq::RichSeq=3DHASH(0xb820b14)', '-use_magic', 1) called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 353 GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supported::= Plugin::InsertSequenceFeatures=3DHASH(0xa011adc)', 'Bio::Seq::RichSeq=3DHASH(0xb820b14)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 720 GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S= upported::Plugin::InsertSequenceFeatures=3DHASH(0xa011adc)', 'Bio::Seq::RichSeq=3DHASH(0xb820b14)', 140, 177) called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 330 GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin= ::InsertSequenceFeatures=3DHASH(0xa011adc)', 'HASH(0xb047e98)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549 eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu= sApplication=3DHASH(0x9ff0c20)', 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica= tion=3DHASH(0x9ff0c20)', 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication= =3DHASH(0x9ff0c20)', 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication= =3DHASH(0x9ff0c20)', 'ARRAY(0xa004738)') called at /GUS/gus_home/bin/ga line 11 |