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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
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