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[GUSDEV] RES: ISF error
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From: davila <da...@io...> - 2007-05-12 16:39:48
|
Thanks Steve !
I will open the script and check it, however, is this a GUS plugin : =
"GUS::Supported::UnflattenBioperlFeatures::preprocess" ? if so, it is =
not available at $GUS_HOME or $PROJECT_HOME plugin directories:
[davila1@kineto4 Supported]$ ls -lh =
$PROJECT_HOME/GUS/Supported/plugin/perl/
total 668K
-rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
-rw-r--r-- 1 davila1 gus 12K May 3 17:12 =
CalculateTranslatedAASequences.pm
-rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
-rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
-rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
-rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
-rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
-rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
-rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 =
InsertOntologyRelationshipType.pm
-rw-r--r-- 1 davila1 gus 16K May 3 17:12 =
InsertOntologyTermsAndRelationships.pm
-rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
-rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
-rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
-rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
-rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
-rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
-rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
-rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
-rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
-rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
-rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
drwxr-xr-x 3 davila1 gus 4.0K May 3 17:12 Test
[davila1@kineto4 Supported]$ ls -lh =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/
total 668K
-rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
-rw-r--r-- 1 davila1 gus 12K May 3 17:12 =
CalculateTranslatedAASequences.pm
-rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
-rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
-rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
-rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
-rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
-rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
-rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 =
InsertOntologyRelationshipType.pm
-rw-r--r-- 1 davila1 gus 16K May 3 17:12 =
InsertOntologyTermsAndRelationships.pm
-rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
-rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
-rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
-rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
-rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
-rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
-rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
-rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
-rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
-rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
-rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
drwxr-xr-x 2 davila1 gus 4.0K May 3 17:12 Test
This is the part of the =
"$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm" plugin =
originating the error:
sub preprocessBioperlSeq {
my ($self, $bioperlSeq) =3D @_;
return unless $self->{bioperlSeqPreprocessor};
my $class =3D $self->{bioperlSeqPreprocessor}->{class};
eval {
no strict "refs";
eval "require $class";
my $method =3D "${class}::preprocess";
&$method($bioperlSeq); ### Line 63 originating the error #####
};
my $err =3D $@;
if ($err) { die "Can't run bioperlSeq preprocessor method =
'${class}::preprocess'. Error:\n $err\n"; }
}
Where I can find "$bioperlSeq" ?
Thanks, Alberto
-----Mensagem original-----
De: Steve Fischer [mailto:sfi...@pc...]
Enviada: sex 11-mai-07 3:01
Para: davila
Cc: gus...@li...; mro...@cs...; =
cj...@fr...
Assunto: Re: [GUSDEV] ISF error
=20
it looks as though it is trying to find the taxon of the sequence but is =
coming up with a null (see the method getTaxonId in the plugin).
if the file contains all one species, you can provide that on the=20
command line.
otherwise, you'll need to look at the plugin code to see where in the=20
files it is expecting to find that info and correct the files so that it =
is there.
steve
davila wrote:
>
> Hi Folks, could anyone help to debug this error ?
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir=20
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank=20
> --extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=3Dmydb
> Fri May 11 13:20:31 2007 PLUGIN =20
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:20:31 2007 ARG algoinvo 1
> Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:20:31 2007 ARG comment
> Fri May 11 13:20:31 2007 ARG commit 0
> Fri May 11 13:20:31 2007 ARG debug 0
> Fri May 11 13:20:31 2007 ARG defaultOrganism
> Fri May 11 13:20:31 2007 ARG extDbName GenBank
> Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 ARG fileFormat genbank
> Fri May 11 13:20:31 2007 ARG gff2GroupTag
> Fri May 11 13:20:31 2007 ARG group
> Fri May 11 13:20:31 2007 ARG gusconfigfile =20
> $GUS_HOME/config/gus.config
> Fri May 11 13:20:31 2007 ARG handlerExternalDbs
> Fri May 11 13:20:31 2007 ARG help
> Fri May 11 13:20:31 2007 ARG helpHTML
> Fri May 11 13:20:31 2007 ARG inputFileExtension
> Fri May 11 13:20:31 2007 ARG inputFileOrDir =20
> /home/davila1/lguyanensis.gb
> Fri May 11 13:20:31 2007 ARG mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:20:31 2007 ARG naSequenceSubclass
> Fri May 11 13:20:31 2007 ARG organism
> Fri May 11 13:20:31 2007 ARG project
> Fri May 11 13:20:31 2007 ARG seqExtDbName
> Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
> Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
> Fri May 11 13:20:31 2007 ARG seqSoTerm
> Fri May 11 13:20:31 2007 ARG seqType
> Fri May 11 13:20:31 2007 ARG soCvsVersion
> Fri May 11 13:20:31 2007 ARG sqlVerbose 0
> Fri May 11 13:20:31 2007 ARG testNumber
> Fri May 11 13:20:31 2007 ARG user
> Fri May 11 13:20:31 2007 ARG verbose 0
> Fri May 11 13:20:31 2007 ARG veryVerbose 0
> Fri May 11 13:20:31 2007 AlgInvocationId 61
> Fri May 11 13:20:31 2007 COMMIT commit off
> Fri May 11 13:20:31 2007 Processing file=20
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Attempting to get id from cache with null name at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
> 1103, <GEN32> line 65.
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm=20
> line 1103
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supp=
orted::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',=20
> 'taxon_id') called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
998
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supporte=
d::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)') called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
645
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS:=
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
604
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
574
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Sup=
ported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
361
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'HASH(0x20628f0)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
> However, when I use --organism and --defaultOrganism the error =
changes:
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir=20
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank=20
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"=20
> --defaultOrganism "Leishmania guyanensis" --verbose
> Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=3Dmydb
> Fri May 11 13:21:54 2007 PLUGIN =20
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:21:54 2007 ARG algoinvo 1
> Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:21:54 2007 ARG comment
> Fri May 11 13:21:54 2007 ARG commit 0
> Fri May 11 13:21:54 2007 ARG debug 0
> Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania=20
> guyanensis
> Fri May 11 13:21:54 2007 ARG extDbName GenBank
> Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:21:54 2007 ARG fileFormat genbank
> Fri May 11 13:21:54 2007 ARG gff2GroupTag
> Fri May 11 13:21:54 2007 ARG group
> Fri May 11 13:21:54 2007 ARG gusconfigfile =20
> $GUS_HOME/config/gus.config
> Fri May 11 13:21:54 2007 ARG handlerExternalDbs
> Fri May 11 13:21:54 2007 ARG help
> Fri May 11 13:21:54 2007 ARG helpHTML
> Fri May 11 13:21:54 2007 ARG inputFileExtension
> Fri May 11 13:21:54 2007 ARG inputFileOrDir =20
> /home/davila1/lguyanensis.gb
> Fri May 11 13:21:54 2007 ARG mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:21:54 2007 ARG naSequenceSubclass
> Fri May 11 13:21:54 2007 ARG organism Leishmania=20
> guyanensis
> Fri May 11 13:21:54 2007 ARG project
> Fri May 11 13:21:54 2007 ARG seqExtDbName
> Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
> Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
> Fri May 11 13:21:54 2007 ARG seqSoTerm
> Fri May 11 13:21:54 2007 ARG seqType
> Fri May 11 13:21:54 2007 ARG soCvsVersion
> Fri May 11 13:21:54 2007 ARG sqlVerbose 0
> Fri May 11 13:21:54 2007 ARG testNumber
> Fri May 11 13:21:54 2007 ARG user
> Fri May 11 13:21:54 2007 ARG verbose 1
> Fri May 11 13:21:54 2007 ARG veryVerbose 0
> Fri May 11 13:21:54 2007 AlgInvocationId 62
> Fri May 11 13:21:54 2007 COMMIT commit off
> Fri May 11 13:21:54 2007 Processing file=20
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Can't run bioperlSeq preprocessor method=20
> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
>
> ERROR:
> Undefined subroutine=20
> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at=20
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,=20
> <GEN32> line 65.
>
> STACK TRACE:
> at=20
> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm=20
> line 63
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
> =20
> =
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)')=20
> called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)',=20
> 'HASH(0x2062960)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
> =20
> =
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)')=20
> called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)',=20
> 'HASH(0x2062960)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
> Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy =
> (*.dmp) file from May 11 2007, apparently it does not make a new load, =
> but updates the respective Sres tables, anyway such as the first run=20
> the re-run of LoadTaxon provided these warnings:
>
> Fri May 11 12:42:27 2007 Merging taxons
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not=20
> in database, skipping
>
> What this exactly means ?
>
> The first time I ran LoadTaxon I got this log:
>
> tail LoadTaxon.log
> Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
> Mon May 7 00:07:39 2007 0 TaxonName entries deleted
>
> Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
> Mon May 7 00:07:42 2007 RESULT 1
> Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
> Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
> Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
> Mon May 7 00:07:47 2007 AlgInvocationId 7
> Mon May 7 00:07:47 2007 COMMIT commit on
>
> The second time:
>
> tail LoadTaxon_new.log
> Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
> Fri May 11 13:07:51 2007 288 TaxonName entries deleted
>
> Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
> Fri May 11 13:07:55 2007 RESULT 1
> Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
> Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
> Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
> Fri May 11 13:07:56 2007 AlgInvocationId 56
> Fri May 11 13:07:56 2007 COMMIT commit on
>
> I just checked the sres.taxonname and it has Leishmania guyanensis =
there:
>
> SELECT=20
> =
"taxon_name_id","taxon_id","name","unique_name_variant","name_class","mod=
ification_date","row_project_id","row_alg_invocation_id"=20
> FROM "sres"."taxonname" WHERE
> "name" =3D 'Leishmania guyanensis';
> taxon_name_id | taxon_id | name |=20
> unique_name_variant | name_class | modification_date |=20
> row_project_id | row_alg_invocation_id
> =
---------------+----------+-----------------------+---------------------+=
-----------------+---------------------------+----------------+----------=
-------------
> 369208 | 96595 | Leishmania guyanensis=20
> | | scientific name | 2007-05-06 23:41:16.98889=20
> | 1 | 7
> (1 row)
>
> According to the log, it could be an=20
> UnflattenBioperlFeatures::preprocess error too...
>
> Some of th GIs (L. guyanensis) I am trying to load with the ISF=20
> pluging are:
>
> 104530485
> 60280340
> 110816091
> 76577720
> 76577719
> 76577718
>
> Thanks for any help you might provide.
>
> Cheers, Alberto
>
|
