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RE: [GUSDEV] Problem in running "InsertSequenceFeatures.pm'
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From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-31 15:04:10
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Hi Steve,
Thanks for your reply.Even after using new genbank2gus.xml file it
requires SO=20
definition data in the SRES.SequenceOntology table.
Any way, I downloaded the SO definition data and loaded in the system
using
InsertSequenceOntology.pm.
Problem noticed in tn loading SO data :
1. Field size in SRES.sequenceOntology table for "definition" column
is 255, which is=20
insufficient to hold some of definition whose size is about 1004.=20
So, pl. take appropriate action to increase the field size for
future GUS releases.
2. Even after the plugin was failing, it loaded data partially in the
table.
(I think it should rollback entirely)
Again back to InsertSequenceFeatures plugin, it is failing even after
loading the
sequence ontology data. This time it is throwing error message
mentioned below.
It looks to me that this pluin requires some master data in the
system prior to run,
Do we have any kind of writeup about the prerequisite data.
[oragus35@rdevse02 oragus35]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --seqFile
/u02/Downloads/data/Fra6570.genbank --mapFile
/home/oragus35/genbank2gus.xml --fileFormat 'genbank' --extDbName
'genBank' --extDbRlsVer 147 --soCvsVersion 3354
Wed Aug 31 10:58:36 2005 ARGS algoinvo 1
Wed Aug 31 10:58:36 2005 ARGS comment
Wed Aug 31 10:58:36 2005 ARGS commit 0
Wed Aug 31 10:58:36 2005 ARGS debug 0
Wed Aug 31 10:58:36 2005 ARGS description
Wed Aug 31 10:58:36 2005 ARGS downloadURL
Wed Aug 31 10:58:36 2005 ARGS extDbName genBank
Wed Aug 31 10:58:36 2005 ARGS extDbRlsDate
Wed Aug 31 10:58:36 2005 ARGS extDbRlsVer 147
Wed Aug 31 10:58:36 2005 ARGS failDir
Wed Aug 31 10:58:36 2005 ARGS fileFormat genbank
Wed Aug 31 10:58:36 2005 ARGS filename
Wed Aug 31 10:58:36 2005 ARGS gff2GroupTag GenePrediction
Gene
Wed Aug 31 10:58:36 2005 ARGS gffFormat 2
Wed Aug 31 10:58:36 2005 ARGS group
Wed Aug 31 10:58:36 2005 ARGS gusconfigfile =20
/home/oragus35/GUS/gus.properties
Wed Aug 31 10:58:36 2005 ARGS help
Wed Aug 31 10:58:36 2005 ARGS helpHTML
Wed Aug 31 10:58:36 2005 ARGS isUpdateMode 0
Wed Aug 31 10:58:36 2005 ARGS mapFile=20
/home/oragus35/genbank2gus.xml
Wed Aug 31 10:58:36 2005 ARGS naSequenceSubclass
Wed Aug 31 10:58:36 2005 ARGS project
Wed Aug 31 10:58:36 2005 ARGS projectName
Wed Aug 31 10:58:36 2005 ARGS restartPoint
Wed Aug 31 10:58:36 2005 ARGS seqFile=20
/u02/Downloads/data/Fra6570.genbank
Wed Aug 31 10:58:36 2005 ARGS seqIdColumn source_id
Wed Aug 31 10:58:36 2005 ARGS seqSoTerm
Wed Aug 31 10:58:36 2005 ARGS seqType DNA
Wed Aug 31 10:58:36 2005 ARGS soCvsVersion 3354
Wed Aug 31 10:58:36 2005 ARGS sqlVerbose 0
Wed Aug 31 10:58:36 2005 ARGS testNumber
Wed Aug 31 10:58:36 2005 ARGS user
Wed Aug 31 10:58:36 2005 ARGS verbose 0
Wed Aug 31 10:58:36 2005 ARGS veryVerbose 0
Wed Aug 31 10:58:36 2005 COMMIT commit off
Wed Aug 31 10:58:36 2005 ALGINVID 427
ERROR:
Failed to retrieve GUS::Model::DoTS::SequenceType id for name =3D 'DNA' =
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1063, <GEN0> line 73767.
STACK TRACE:
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1063
=20
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Sup
ported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'seqTypeCache', 'DNA', 'GUS::Model::DoTS::SequenceType', 'name') called
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 800
=20
GUS::Supported::Plugin::InsertSequenceFeatures::getSeqTypeId('GUS::Suppo
rted::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'DNA') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 580
=20
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS
::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'Bio::Seq::RichSeq=3DHASH(0xa064044)', 42) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 547
=20
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS:
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'Bio::Seq::RichSeq=3DHASH(0xa064044)') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 348
=20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
gin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'HASH(0x90288dc)') 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
Thanks
Sanjeev=20
-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Tuesday, August 30, 2005 6:21 PM
To: Kumar, Sanjeev (Contr)
Cc: gus...@li...
Subject: Re: [GUSDEV] Problem in running "InsertSequenceFeatures.pm'
sanjeev-
use this mapping file:
$GUS_HOME/config/genbank2gus.xml
the one you are using is old and is using SO ids instead of SO terms,
which are what is needed.
steve
Kumar, Sanjeev (Contr) wrote:
> Hi,
> Can anyone help me in uns=3Dderstanding and resolving the problem.
> I am getting this problem when I am trying to run and load genbank=20
>sequence file.
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Sanjeev Kumar [mailto:sk...@bi...]
>Sent: Tuesday, August 30, 2005 5:51 PM
>To: Kumar, Sanjeev (Contr)
>Subject: (no subject)
>
>[oragus35@rdevse02 oragus35]$ ga
>GUS::Supported::Plugin::InsertSequenceFeatures --seqFile=20
>/u02/Downloads/data/Fra6570.genbank --mapFile=20
>/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
>--fileFormat 'genbank' --extDbName 'genBank' --extDbRlsVer 147=20
>--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=20
>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::InsertSequen
>c
>eFeatures=3DHASH(0x85bea48)',
>'Mapping file \'/home/oragus35/ApiComplexa/DataLoad/doc/config...')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc
>e
>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/InsertSequenc
>e
>Features.pm
>line 335
> =20
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Pl
>u 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=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
> =20
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApp
>l
>ication=3DHASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
> =20
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplica
>t
>ion=3DHASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
> =20
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplica
>t
>ion=3DHASH(0x811e180)',
>'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line=20
>11
>
>
>
>
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