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From: Aaron J. M. <am...@pc...> - 2006-01-26 17:13:42
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This is a BioPerl "Unflattener" error; it's unable to automatically
reconstruct the gene/mRNA/exon logic of some (or all) of the
annotation in your genbank file. To get help with this, you should
post a message to the BioPerl mailing list (bio...@bi...),
including a snippet of your genbank file.
-Aaron
On Jan 26, 2006, at 11:53 AM, Ricardo Balbi wrote:
> 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 /G
> US/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=HASH(0xb5e124c)',
> '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=HASH(0xb5e124c)', '-seq',
> 'Bio::Seq::RichSeq=HASH(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=HASH(0xa011adc)',
> 'Bio::Seq::RichSeq=HASH(0xb820b14)') called at /GUS/gus_home/lib/
> perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 720
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
> 'Bio::Seq::RichSeq=HASH(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=HASH(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::GusApplication=HASH(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::GusApplication=HASH(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=HASH(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=HASH(0x9ff0c20)', 'ARRAY
> (0xa004738)') called at /GUS/gus_home/bin/ga line 11
>
>
>
--
Dr. Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email: am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
215-746-7018 (PCBI, 1428 Blockley Hall)
fax: 215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
Goddard Labs 212
415 S. University Avenue
Philadelphia, PA 19104-6017
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