[GUSDEV] Problem in running "InsertSequenceFeatures.pm'

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 Hi,
   Can anyone help me in uns=3Dderstanding and resolving the problem.
   I am getting this problem when I am trying to run and load genbank
sequence file.

Thanks
Sanjeev

-----Original Message-----
From: Sanjeev Kumar [mailto:sk...@bi...]=20
Sent: Tuesday, August 30, 2005 5:51 PM
To: Kumar, Sanjeev (Contr)
Subject: (no subject)

[oragus35@rdevse02 oragus35]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --seqFile
/u02/Downloads/data/Fra6570.genbank --mapFile
/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
--fileFormat 'genbank' --extDbName 'genBank' --extDbRlsVer 147
--soCvsVersion 3354
Tue Aug 30 18:10:56 2005        ARGS    algoinvo        1
Tue Aug 30 18:10:56 2005        ARGS    comment
Tue Aug 30 18:10:56 2005        ARGS    commit  0
Tue Aug 30 18:10:56 2005        ARGS    debug   0
Tue Aug 30 18:10:56 2005        ARGS    description
Tue Aug 30 18:10:56 2005        ARGS    downloadURL
Tue Aug 30 18:10:56 2005        ARGS    extDbName       genBank
Tue Aug 30 18:10:56 2005        ARGS    extDbRlsDate
Tue Aug 30 18:10:56 2005        ARGS    extDbRlsVer     147
Tue Aug 30 18:10:56 2005        ARGS    failDir
Tue Aug 30 18:10:56 2005        ARGS    fileFormat      genbank
Tue Aug 30 18:10:56 2005        ARGS    filename
Tue Aug 30 18:10:56 2005        ARGS    gff2GroupTag    GenePrediction
Gene
Tue Aug 30 18:10:56 2005        ARGS    gffFormat       2
Tue Aug 30 18:10:56 2005        ARGS    group
Tue Aug 30 18:10:56 2005        ARGS    gusconfigfile  =20
/home/oragus35/GUS/gus.properties
Tue Aug 30 18:10:56 2005        ARGS    help
Tue Aug 30 18:10:56 2005        ARGS    helpHTML
Tue Aug 30 18:10:56 2005        ARGS    isUpdateMode    0
Tue Aug 30 18:10:56 2005        ARGS    mapFile=20
/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
Tue Aug 30 18:10:56 2005        ARGS    naSequenceSubclass
Tue Aug 30 18:10:56 2005        ARGS    project
Tue Aug 30 18:10:56 2005        ARGS    projectName
Tue Aug 30 18:10:56 2005        ARGS    restartPoint
Tue Aug 30 18:10:56 2005        ARGS    seqFile=20
/u02/Downloads/data/Fra6570.genbank
Tue Aug 30 18:10:56 2005        ARGS    seqIdColumn     source_id
Tue Aug 30 18:10:56 2005        ARGS    seqSoTerm
Tue Aug 30 18:10:56 2005        ARGS    seqType DNA
Tue Aug 30 18:10:56 2005        ARGS    soCvsVersion    3354
Tue Aug 30 18:10:56 2005        ARGS    sqlVerbose      0
Tue Aug 30 18:10:56 2005        ARGS    testNumber
Tue Aug 30 18:10:56 2005        ARGS    user
Tue Aug 30 18:10:56 2005        ARGS    verbose 0
Tue Aug 30 18:10:56 2005        ARGS    veryVerbose     0
Tue Aug 30 18:10:56 2005        COMMIT  commit off
Tue Aug 30 18:10:56 2005        ALGINVID        406

ERROR:

USER ERROR: Mapping file
'/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml' or cmd
line args are using the following SO terms that are not found in the
database for SO CVS version '3354': SO:0000297, SO:0000234, SO:0000725,
SO:0000110, SO:0000704, SO:0000172, SO:0000418, SO:0000204, SO:0000557,
SO:0000313, SO:0000141, SO:0000298, SO:0000657, SO:0000176, SO:0000185,
SO:0000013, SO:0005836, SO:0000413, SO:0000173, SO:0000275, SO:0000140,
SO:0000331, SO:0000274, SO:0000555, SO:0000188, SO:0000252, SO:0000167,
SO:0000005, SO:0000410, SO:0000109, SO:0000492, SO:0000139, SO:0000174,
SO:0000286, SO:0000673, SO:0000724, SO:0000178, SO:0000553, SO:0000563,
SO:0000305, SO:0000147, SO:0000253, SO:0000478, SO:0000205, SO:0000723,
SO:0000316, SO:0000302, SO:0000413, SO:0005850, SO:0000296, SO:0000185,
SO:0000551, SO:0000175, SO:0000409, SO:0000419, SO:0000002

STACK TRACE:
 at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line
1189
       =20
GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertSequenc
eFeatures=3DHASH(0x85bea48)',
'Mapping file \'/home/oragus35/ApiComplexa/DataLoad/doc/config...')
called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1108
       =20
GUS::Supported::Plugin::InsertSequenceFeatures::getSoPrimaryKeys('GUS::S
upported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)')
called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 335
       =20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
gin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'HASH(0x902894c)') 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(0x811e180)',
'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(0x811e180)',
'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(0x811e180)',
'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(0x811e180)',
'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line 11