[Bioperl-l] [GUSDEV] Another error executing ISF

[Ricardo Balbi]

Hi all,

   Anybody could help me with this error ?

thanks in advance,
Ricardo

2006/1/26, Aaron J. Mackey <amackey at pcbi.upenn.edu>:
>
>
> 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 (bioperl-l at bioperl.org),
> 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:  amackey at pcbi.upenn.edu
> 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
>
>
>