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Re: [GUSDEV] ISF testing
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From: Steve F. <sfi...@pc...> - 2005-09-23 23:19:15
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henrique-
oops, sorry about that. it was under a bit of construction today. you=20
caught it when it was temporarily broken. get the latest, which fixes=20
that problem. (it will have occasional problems like this as it=20
continues to stabilize of the next week or so)
as always, be sure to get all of GUS/Supported, not just that one file.
steve
Henrique Juc=E1 wrote:
>Hi,
>
>Trying to test ISF plugin. This is the output I received....
>
>[juca@desterrensis Plugin]$ ga
>GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
>/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile
>/home/juca/GUS-Files/ISF/Z_mobilis.fasta --fileFormat genbank
>--extDbName 'TESTE' --extDbRlsVer '2005-09-06' --soCvsVersion 1.42
>Fri Sep 23 17:10:01 2005 ARGS algoinvo 1
>Fri Sep 23 17:10:01 2005 ARGS comment
>Fri Sep 23 17:10:01 2005 ARGS commit 0
>Fri Sep 23 17:10:01 2005 ARGS debug 0
>Fri Sep 23 17:10:01 2005 ARGS defaultOrganism
>Fri Sep 23 17:10:01 2005 ARGS description
>Fri Sep 23 17:10:01 2005 ARGS downloadURL
>Fri Sep 23 17:10:01 2005 ARGS extDbName TESTE
>Fri Sep 23 17:10:01 2005 ARGS extDbRlsDate
>Fri Sep 23 17:10:01 2005 ARGS extDbRlsVer 2005-09-06
>Fri Sep 23 17:10:01 2005 ARGS failDir
>Fri Sep 23 17:10:01 2005 ARGS fileFormat genbank
>Fri Sep 23 17:10:01 2005 ARGS filename
>Fri Sep 23 17:10:01 2005 ARGS gff2GroupTag GenePrediction =
Gene
>Fri Sep 23 17:10:01 2005 ARGS gffFormat 2
>Fri Sep 23 17:10:01 2005 ARGS group
>Fri Sep 23 17:10:01 2005 ARGS gusconfigfile =20
>/usr/local/GUS/gus.properties
>Fri Sep 23 17:10:01 2005 ARGS help
>Fri Sep 23 17:10:01 2005 ARGS helpHTML
>Fri Sep 23 17:10:01 2005 ARGS isUpdateMode 0
>Fri Sep 23 17:10:01 2005 ARGS mapFile
>/home/juca/GUS-Files/ISF/genbank2gus.xml
>Fri Sep 23 17:10:01 2005 ARGS naSequenceSubclass
>Fri Sep 23 17:10:01 2005 ARGS project
>Fri Sep 23 17:10:01 2005 ARGS projectName
>Fri Sep 23 17:10:01 2005 ARGS restartPoint
>Fri Sep 23 17:10:01 2005 ARGS seqFile
>/home/juca/GUS-Files/ISF/Z_mobilis.fasta
>Fri Sep 23 17:10:01 2005 ARGS seqIdColumn source_id
>Fri Sep 23 17:10:01 2005 ARGS seqSoTerm
>Fri Sep 23 17:10:01 2005 ARGS seqType
>Fri Sep 23 17:10:01 2005 ARGS soCvsVersion 1.42
>Fri Sep 23 17:10:01 2005 ARGS sqlVerbose 0
>Fri Sep 23 17:10:01 2005 ARGS testNumber
>Fri Sep 23 17:10:01 2005 ARGS user
>Fri Sep 23 17:10:01 2005 ARGS verbose 0
>Fri Sep 23 17:10:01 2005 ARGS veryVerbose 0
>Fri Sep 23 17:10:01 2005 COMMIT commit off
>Fri Sep 23 17:10:01 2005 ALGINVID 104
>
>ERROR:
>Cannot import or construct new object for qualifier handler class
>'GUS::Supported::SpecialCaseQualifierHandlers'
>Can't modify constant item in scalar assignment at (eval 24) line 1, nea=
r "))"
>Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
>while "strict subs" in use at (eval 24) line 1.
>
>STACK TRACE:
> at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.=
pm
>line 73 GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS:=
:Supported::BioperlFeatMapperSet=3DHASH(0x9486
>68c)', '/home/juca/GUS-Files/ISF/genbank2gus.xml',
>'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a2 4160)')
>called at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapp=
erSet.pm
>line 17 GUS::Supported::BioperlFeatMapperSet::new('GUS::Supported=
::BioperlFeatMapperSet',
>'/home/juca/GUS-Fil es/ISF/genbank2gus.xml',
>'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a24160)')
>called at /usr/loc
>al/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>line 335 =20
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu=
gin::InsertSequenceFeatures=3DH
>ASH(0x8a24160)', 'HASH(0x9486608)') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.p m line
>469
>eval {...} called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
>461 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS:=
:PluginMgr::GusApplication=3DHASH(0x84d7c2
>0)', 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>/usr/local/GUS/gus_home/lib/perl/GUS/Plug inMgr/GusApplication.pm line
>380 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginM=
gr::GusApplication=3DHASH(0x84d7c20)',
>'GU S::Supported::Plugin::InsertSequenceFeatures') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusAp plication.pm line
>288 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d7c20)',
>'GUS::S upported::Plugin::InsertSequenceFeatures') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplic ation.pm line
>197 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d7c20)',
>'ARRAY( 0x84eb568)') called at /usr/local/GUS/gus_home/bin/ga line 11
>
>
>Hope it helps debugging...
>
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
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