Re: [GUSDEV] ISF error in loading influenza sequence

[Kumar, S. <San...@ng...>]

Hi Steve,
  The file is small genBank file. Let me attach the file.
  And the command I am using to load is as follows:
ga GUS::Supported::Plugin::InsertSequenceFeatures --seqFile $loadFile
--mapFile /home/oragus35/genbank2gus.xml --fileFormat 'genbank'
--extDbName $database --extDbRlsVer $dbVersion --soCvsVersion 3354
--gusconfigfile /home/oragus35/GUS/gus.properties --commit
2>>$outputFile`;

Thanks
Sanjeev


-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Friday, July 07, 2006 5:54 PM
To: Kumar, Sanjeev
Cc: gus...@li...
Subject: Re: [GUSDEV] ISF error in loading influenza sequence

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=20
> 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.
>    =20
> =20
> Thanks
> Sanjeev Kumar
> Northrop Grumman
> =20
>  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/InsertSequence
Features.pm:383
>     STACK GUS::Supported::Plugin::InsertSequenceFeatures::run
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.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=20
> 342
>           =20
>
Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=3DHASH(0xa237=
d
08)',
>     'structure_type 2 is currently unknown') called at
>
/home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener
.pm
>     line 1419
>           =20
>
Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Too
ls::Unflattener=3DHASH(0xa237d08)',
>     '-seq', 'Bio::Seq::RichSeq=3DHASH(0x9febe2c)', '-use_magic', 1)
>     called at
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
>     line 383
>           =20
>
GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supporte
d::Plugin::InsertSequenceFeatures=3DHASH(0x9414bf0)',
>     'Bio::Seq::RichSeq=3DHASH(0x9febe2c)') called at
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
>     line 358
>           =20
>
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
gin::InsertSequenceFeatures=3DHASH(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
>           =20
>
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
:GusApplication=3DHASH(0x8f74180)',
>     'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>     line 380
>           =20
>
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
ication=3DHASH(0x8f74180)',
>     'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>     line 288
>           =20
>
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x8f74180)',
>     'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>     line 197
>           =20
>
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x8f74180)',
>     'ARRAY(0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga
>     line 11
>     =20
>
> =20
> =20
> ----------------------------------------------------------------------
> --
>
> Using Tomcat but need to do more? Need to support web services,
security?
> Get stuff done quickly with pre-integrated technology to make your job

> easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> Apache Geronimo
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
1216
> 42
> ----------------------------------------------------------------------
> --
>
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  =20