Re: [GUSDEV] ISF error in loading influenza sequence

[Mark S. H. <mh...@ug...>]

See
http://lists.open-bio.org/pipermail/bioperl-l/2006-January/020687.html
where this error was diagnosed as a BioPerl Unflattener issue.

Even if it does not directly solve your problem perhaps you can take  
comfort in knowing you are not alone. :-(

-Mark

Mark Heiges
CryptoDB.org
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
TEL:  +1 (706) 542-1447


On Jul 7, 2006, at 5:39 PM, Kumar, Sanjeev wrote:

> Hi Group,
>     I am getting following error when I am trying to load one  
> influenza sequence using "InsertSequenceFeature' plugin.
>     I am not able to figure out the reason of the failure. I need  
> your assistance, any help will be appreciated.
>     The sequence file is attached.
>
>
> Thanks
> Sanjeev Kumar
> Northrop Grumman
>
>  ERROR:
> ------------- EXCEPTION  -------------
> MSG: structure_type 2 is currently unknown
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /home/ 
> oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/ 
> Unflattener.pm:1419
> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten / 
> home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm:383
> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /home/ 
> oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm:358
> STACK (eval) /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication.pm:469
> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /home/ 
> oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461
> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /home/ 
> oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380
> STACK GUS::PluginMgr::GusApplication::doMajorMode /home/oragus35/ 
> GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288
> STACK GUS::PluginMgr::GusApplication::parseAndRun /home/oragus35/ 
> GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197
> STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11
> --------------------------------------
> STACK TRACE:
>  at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line 342
>         Bio::Root::Root::throw 
> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)',  
> 'structure_type 2 is currently unknown') called at /home/oragus35/ 
> perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener.pm line 1419
>         Bio::SeqFeature::Tools::Unflattener::unflatten_seq 
> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)', '-seq',  
> 'Bio::Seq::RichSeq=HASH(0x9febe2c)', '-use_magic', 1) called at / 
> home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm line 383
>         GUS::Supported::Plugin::InsertSequenceFeatures::unflatten 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)',  
> 'Bio::Seq::RichSeq=HASH(0x9febe2c)') called at /home/oragus35/GUS/ 
> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm  
> line 358
>         GUS::Supported::Plugin::InsertSequenceFeatures::run 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)',  
> 'HASH(0x9ef7284)') called at /home/oragus35/GUS/gus_home/lib/perl/ 
> GUS/PluginMgr/GusApplication.pm line 469
>         eval {...} called at /home/oragus35/GUS/gus_home/lib/perl/ 
> GUS/PluginMgr/GusApplication.pm line 461
>         GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport 
> ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at / 
> home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm  
> line 380
>         GUS::PluginMgr::GusApplication::doMajorMode_Run 
> ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /home/ 
> oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
> 288
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /home/ 
> oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
> 197
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', 'ARRAY 
> (0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga line 11
>
>
>
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