Re: [GUSDEV] ISF error in loading influenza sequence

[Steve F. <sfi...@pc...>]

sanjeev-

how big is the file you are trying to load?  i want to take a look at 
it.  is it in genbank?  what is its accession?

can you send the command line?


steve

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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