gusdev-gusdev

[GUSDEV] Another error executing ISF

[Ricardo B. <rb...@gm...>]

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

Re: [GUSDEV] Another error executing ISF

[Aaron J. M. <am...@pc...>]

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