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Re: [GUSDEV] Problem in running "InsertSequenceFeatures.pm'
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From: Steve F. <sfi...@pc...> - 2005-08-30 22:21:26
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sanjeev-
use this mapping file:
$GUS_HOME/config/genbank2gus.xml
the one you are using is old and is using SO ids instead of SO terms,
which are what is needed.
steve
Kumar, Sanjeev (Contr) wrote:
> Hi,
> Can anyone help me in uns=derstanding and resolving the problem.
> I am getting this problem when I am trying to run and load genbank
>sequence file.
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Sanjeev Kumar [mailto:sk...@bi...]
>Sent: Tuesday, August 30, 2005 5:51 PM
>To: Kumar, Sanjeev (Contr)
>Subject: (no subject)
>
>[oragus35@rdevse02 oragus35]$ 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
>/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
>/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
>/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
>
>GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertSequenc
>eFeatures=HASH(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
>
>GUS::Supported::Plugin::InsertSequenceFeatures::getSoPrimaryKeys('GUS::S
>upported::Plugin::InsertSequenceFeatures=HASH(0x85bea48)')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm
>line 335
>
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
>gin::InsertSequenceFeatures=HASH(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
>
>GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
>:GusApplication=HASH(0x811e180)',
>'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::GusAppl
>ication=HASH(0x811e180)',
>'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::GusApplicat
>ion=HASH(0x811e180)',
>'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::GusApplicat
>ion=HASH(0x811e180)',
>'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line 11
>
>
>
>
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