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Re: [GUSDEV] ISF error
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From: Steve F. <sfi...@pc...> - 2007-05-11 18:02:05
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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
command line.
otherwise, you'll need to look at the plugin code to see where in the
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
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=mydb
> Fri May 11 13:20:31 2007 PLUGIN
> 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
> $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
> /home/davila1/lguyanensis.gb
> Fri May 11 13:20:31 2007 ARG mapFile
> $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
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Attempting to get id from cache with null name at
> $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
> line 1103
>
> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
> 'taxon_id') called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 998
>
> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 645
>
> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 604
>
> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 574
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 361
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'HASH(0x20628f0)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> '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
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
> --defaultOrganism "Leishmania guyanensis" --verbose
> Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=mydb
> Fri May 11 13:21:54 2007 PLUGIN
> 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
> 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
> $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
> /home/davila1/lguyanensis.gb
> Fri May 11 13:21:54 2007 ARG mapFile
> $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
> 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
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Can't run bioperlSeq preprocessor method
> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
>
> ERROR:
> Undefined subroutine
> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
> <GEN32> line 65.
>
> STACK TRACE:
> at
> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
> line 63
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
>
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 365
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> 'HASH(0x2062960)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
>
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 365
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> 'HASH(0x2062960)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> '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
> 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
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not
> 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
> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
> FROM "sres"."taxonname" WHERE
> "name" = 'Leishmania guyanensis';
> taxon_name_id | taxon_id | name |
> unique_name_variant | name_class | modification_date |
> row_project_id | row_alg_invocation_id
> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
> 369208 | 96595 | Leishmania guyanensis
> | | scientific name | 2007-05-06 23:41:16.98889
> | 1 | 7
> (1 row)
>
> According to the log, it could be an
> UnflattenBioperlFeatures::preprocess error too...
>
> Some of th GIs (L. guyanensis) I am trying to load with the ISF
> pluging are:
>
> 104530485
> 60280340
> 110816091
> 76577720
> 76577719
> 76577718
>
> Thanks for any help you might provide.
>
> Cheers, Alberto
>
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