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From: Steve F. <sfi...@pc...> - 2007-05-18 16:16:34
|
alberto-
the code is trying to insert a database cross reference to HSSP. to do
this it must create rows in ExternalDatabase and ExternaDatabaseRelease.
the problem is that when it tries to insert a row into ExternalDatabase,
it is using a primary key (18) that is already in use in that table.
the first guesses are that:
- there is something wrong with the database mechanism (postgres) to
generate sequential primary keys
- somebody manually inserted a row into that table, using 18 as a
primary key, without incrementing the primary key generating mechanism
steve
Alberto Davila wrote:
> Hi folks !
>
> We managed to pass several errors with ISF but this one is a bit strange:
>
> [davila1@kineto4 log]$ ga
> GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> /system/GUS/gus_home/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
> --defaultOrganism "Leishmania guyanensis" --verbose --soCvsVersion 1.45
> Fri May 18 12:42:57 2007 DSN dbi:Pg:dbname=protozoa
> Fri May 18 12:42:57 2007 PLUGIN
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 18 12:42:57 2007 ARG algoinvo 1
> Fri May 18 12:42:57 2007 ARG bioperlTreeOutput 0
> Fri May 18 12:42:57 2007 ARG comment
> Fri May 18 12:42:57 2007 ARG commit 0
> Fri May 18 12:42:57 2007 ARG debug 0
> Fri May 18 12:42:57 2007 ARG defaultOrganism Leishmania
> guyanensis
> Fri May 18 12:42:57 2007 ARG extDbName GenBank
> Fri May 18 12:42:57 2007 ARG extDbRlsVer 159.0
> Fri May 18 12:42:57 2007 ARG fileFormat genbank
> Fri May 18 12:42:57 2007 ARG gff2GroupTag
> Fri May 18 12:42:57 2007 ARG group
> Fri May 18 12:42:57 2007 ARG gusconfigfile
> /system/GUS/gus_home/config/gus.config
> Fri May 18 12:42:57 2007 ARG handlerExternalDbs
> Fri May 18 12:42:57 2007 ARG help
> Fri May 18 12:42:57 2007 ARG helpHTML
> Fri May 18 12:42:57 2007 ARG inputFileExtension
> Fri May 18 12:42:57 2007 ARG inputFileOrDir
> /home/davila1/lguyanensis.gb
> Fri May 18 12:42:57 2007 ARG mapFile
> /system/GUS/gus_home/config/genbank2gus.xml
> Fri May 18 12:42:57 2007 ARG naSequenceSubclass
> Fri May 18 12:42:57 2007 ARG organism Leishmania
> guyanensis
> Fri May 18 12:42:57 2007 ARG project
> Fri May 18 12:42:57 2007 ARG seqExtDbName
> Fri May 18 12:42:57 2007 ARG seqExtDbRlsVer
> Fri May 18 12:42:57 2007 ARG seqIdColumn source_id
> Fri May 18 12:42:57 2007 ARG seqSoTerm
> Fri May 18 12:42:57 2007 ARG seqType
> Fri May 18 12:42:57 2007 ARG soCvsVersion 1.45
> Fri May 18 12:42:57 2007 ARG sqlVerbose 0
> Fri May 18 12:42:57 2007 ARG testNumber
> Fri May 18 12:42:57 2007 ARG user
> Fri May 18 12:42:57 2007 ARG verbose 1
> Fri May 18 12:42:57 2007 ARG veryVerbose 0
> Fri May 18 12:42:57 2007 AlgInvocationId 83
> Fri May 18 12:42:57 2007 COMMIT commit off
> Fri May 18 12:42:58 2007 Processing file
> '/home/davila1/lguyanensis.gb'...
> DBD::Pg::st execute failed: ERROR: duplicate key violates unique
> constraint "pk_externaldatabase"
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.ExternalDatabase ( group_write, other_read,
> group_read, name, user_read, row_user_id, external_database_id,
> modification_date, other_write, row_alg_invocation_id, row_project_id,
> row_group_id, user_write )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
> Values: 1, 1, 1, HSSP, 1, 1, 18, 0, 83, 1, 1, 1 at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
> SRes.ExternalDataba...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
> '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write,
> other_...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
> 'HASH(0x30d4870)') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>
> GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 160
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 134
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 117
>
> GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 106
>
> GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
> 'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 1021
>
> GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 891
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 771
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 367
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HASH(0x2062a70)') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> /system/GUS/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
> /system/GUS/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
> /system/GUS/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
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
>
> STACK TRACE:
> at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
> SRes.ExternalDataba...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
> '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write,
> other_...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
> 'HASH(0x30d4870)') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>
> GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 160
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 134
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 117
>
> GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 106
>
> GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
> 'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 1021
>
> GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 891
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 771
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 367
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HASH(0x2062a70)') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> /system/GUS/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
> /system/GUS/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
> /system/GUS/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
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
>
> This is my external_database table:
>
> -- PostgreSQL database dump
> --
>
> SET client_encoding = 'UTF8';
> SET standard_conforming_strings = off;
> SET check_function_bodies = false;
> SET client_min_messages = warning;
> SET escape_string_warning = off;
>
> SET search_path = sres, pg_catalog;
>
>
> COPY externaldatabase (external_database_id, name, modification_date,
> user_read, user_write, group_read, group_write, other_read,
> other_write, row_user_id, row_group_id, row_project_id,
> row_alg_invocation_id) FROM stdin;
> 164 RepBase 4.03 zebrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 106 maize-2dpage 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 2093 homstrad 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 89 mim 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1 assembly 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 154 RepBase 4.03 celrep.ref 4.0.4 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 82 mendel 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 185 RIKEN/FANTOM 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 292 Plasmodium_GSS 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 102 hsc-2dpage 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 2096 PRODOM 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 189 COMPEL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3010 GeneDB_Lmajor 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 2095 load 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 97 subtilist 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 90 mgd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 17 GSDB 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 92 aarhus/ghent-2dpage 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 8 Brookhaven Protein Data Bank (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 184 ORNL GRAILExp gene predictions 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 12 GenPept 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 692 Plasmodium_TIGR 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 144 flybase translated orfs 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 3008 GeneDB_Afumigatus 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 165 RepBase 4.03 humsub.ref 1.0.2 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 13 IMAGE 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 94 ecogene 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3024 GOA 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3011 GeneDB_Pberghei 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3018 GeneDB_Bpertussis 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 1392 CDD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3 EMBL Data Library (nrdb) 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 2097 PFAMA 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 172 URL 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 108 hiv 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 101 stygene 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3014 GeneDB_Tannulata 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 181 Signaling PAthway Database (SPAD) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 10 GenInfo Backbone Id (nrdb) 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 2092 dbSNP 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 78 embl 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 84 prosite 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3025 PubMed 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 6 Protein Research Foundation (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 928 GI 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 85 flybase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 14 EGAD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 126 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1792 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 156 RepBase 4.03 humrep.ref 7.0.6 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 152 TUBERCULIST 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3005 GOC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 392 EPCon 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1892 PID 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 98 eco2dbase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 104 transfac 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 293 Plasmodium_EST 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 127 sptrembl 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 130 imgt/ligm 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1292 RATMAP 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1192 ATCC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3001 GO Function 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 124 SWISS-PROT 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1494 CDD-Pfam 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 143 NCBI genomic Homo Sapiens 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 18 DOTS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 133 estlib 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 161 RepBase 4.03 rodrep.ref 3.3.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 157 RepBase 4.03 invrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 1495 CDD-Smart 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 79 pfam 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 103 carbbank 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 191 Whitehead Institute/MIT Center for Genome Research Mouse RH
> Map 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1
> 1 1 3
> 155 RepBase 4.03 drorep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 125 PSEUDO 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3006 GeneDB_Spombe 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3022 PMID 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 153 RepBase 4.03 athrep.ref 4.0.5 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 122 SPTREMBL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 186 UCSC human draft genomic sequence (October 7 release)
> 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1
> 1 3
> 179 GeneMap 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 135 agis 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3013 GeneDB_Pfalciparum 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 170 Pfam expert 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 178 StemCellDB public 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 149 Bucan lab. mouse BAC ends 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 148 Prodom 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3012 GeneDB_Pchabaudi 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 128 pseudo 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 175 INTERPRO 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 80 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3002 GO Component 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 21 gss_human_bak.seq 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 1293 RGD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 9 Patents (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 15 BLOCKS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 37 swissprot 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 2 GenBank (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 20 dbEST 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 166 Demeter 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 5 NBRF PIR (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 81 pir 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 95 tigr 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1692 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 16 PRINTS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 83 hssp 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3009 GeneDB_Ddiscoideum 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 163 RepBase 4.03 vrtrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 3017 GeneDB_Bparapertussis 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 87 wormpep 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 151 Plasmodium_RoosLab 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3016 GeneDB_Bbronchiseptica 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 146 S. cerevisiae translated orfs 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 182 UCSC human draft genomic sequence (June 15 release)
> 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1
> 1 3
> 4 DDBJ (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 159 RepBase 4.03 plnrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 105 zfin 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 190 TRRD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 2094 cazy 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 22 GenBank 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 140 epd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3019 GeneDB_Styphi 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 145 C.elegans translated orfs 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 162 RepBase 4.03 simple.ref 3.1 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 169 JGI/ORNL contigs 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 88 dictydb 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 173 SCOP 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 793 Derisi Oligos 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 7 Swiss Prot (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3007 GeneDB_Scerevisiae 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 160 RepBase 4.03 pseudo.ref 1.0.5 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 91 swiss-2dpage 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 129 imgt/hla 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 123 taxon 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 100 yepd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 96 sgd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1092 LocusID 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 86 maizedb 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 142 ORNL_grailexp_mrna 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 992 NCBI RefSeq 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3015 GeneDB_Tbrucei 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 147 TIGR mouse BAC ends 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 192 NCBI Malaria Genetics and Genome Project 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 99 gcrdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 11 General database Identifier (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 107 rebase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 180 KEGG: Kyoto Encyclopedia of Genes and Genomes 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 3026 SWALL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 158 RepBase 4.03 mamrep.ref 5.2.2 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 492 Mouse BAC fingerprint map 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 177 Incyte 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 134 gdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 93 pdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3003 GO Process 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 167 Riethman lab. telomere sequences 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 3021 SPTR 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 141 ORNL_genscan_mrna 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3023 TC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 174 SMART 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3020 GeneDB_Gmorsitans 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 139 rzpd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 168 NCBI Reference Sequence (nrdb) 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 1294 COG 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1592 Schwartz Lab Optical Mapping Data 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 19 Unigene_44 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 183 ORNL GenScan gene predictions 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 171 Pfam-B 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 176 MEROPS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 150 Plasmodium_Sanger 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> \.
>
>
> Thanks in advance for any help you might provide ;-)
>
> Cheers, Alberto
>
>
>
>
> davila wrote:
>> 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) = @_;
>> return unless $self->{bioperlSeqPreprocessor};
>> my $class = $self->{bioperlSeqPreprocessor}->{class};
>>
>> eval {
>> no strict "refs";
>> eval "require $class";
>> my $method = "${class}::preprocess";
>> &$method($bioperlSeq); ### Line 63 originating the error #####
>> };
>>
>> my $err = $@;
>> if ($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
>>
>> 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
>> >
>>
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>>
>> This SF.net email is sponsored by DB2 Express
>> Download DB2 Express C - the FREE version of DB2 express and take
>> control of your XML. No limits. Just data. Click to get it now.
>> http://sourceforge.net/powerbar/db2/
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Alberto D. <da...@io...> - 2007-05-18 15:48:04
|
Hi folks !
We managed to pass several errors with ISF but this one is a bit strange:
[davila1@kineto4 log]$ ga GUS::Supported::Plugin::InsertSequenceFeatures
--mapFile /system/GUS/gus_home/config/genbank2gus.xml --inputFileOrDir
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
--extDbRlsVer 159.0 --organism "Leishmania guyanensis" --defaultOrganism
"Leishmania guyanensis" --verbose --soCvsVersion 1.45
Fri May 18 12:42:57 2007 DSN dbi:Pg:dbname=protozoa
Fri May 18 12:42:57 2007 PLUGIN
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 18 12:42:57 2007 ARG algoinvo 1
Fri May 18 12:42:57 2007 ARG bioperlTreeOutput 0
Fri May 18 12:42:57 2007 ARG comment
Fri May 18 12:42:57 2007 ARG commit 0
Fri May 18 12:42:57 2007 ARG debug 0
Fri May 18 12:42:57 2007 ARG defaultOrganism Leishmania
guyanensis
Fri May 18 12:42:57 2007 ARG extDbName GenBank
Fri May 18 12:42:57 2007 ARG extDbRlsVer 159.0
Fri May 18 12:42:57 2007 ARG fileFormat genbank
Fri May 18 12:42:57 2007 ARG gff2GroupTag
Fri May 18 12:42:57 2007 ARG group
Fri May 18 12:42:57 2007 ARG gusconfigfile
/system/GUS/gus_home/config/gus.config
Fri May 18 12:42:57 2007 ARG handlerExternalDbs
Fri May 18 12:42:57 2007 ARG help
Fri May 18 12:42:57 2007 ARG helpHTML
Fri May 18 12:42:57 2007 ARG inputFileExtension
Fri May 18 12:42:57 2007 ARG inputFileOrDir
/home/davila1/lguyanensis.gb
Fri May 18 12:42:57 2007 ARG mapFile
/system/GUS/gus_home/config/genbank2gus.xml
Fri May 18 12:42:57 2007 ARG naSequenceSubclass
Fri May 18 12:42:57 2007 ARG organism Leishmania
guyanensis
Fri May 18 12:42:57 2007 ARG project
Fri May 18 12:42:57 2007 ARG seqExtDbName
Fri May 18 12:42:57 2007 ARG seqExtDbRlsVer
Fri May 18 12:42:57 2007 ARG seqIdColumn source_id
Fri May 18 12:42:57 2007 ARG seqSoTerm
Fri May 18 12:42:57 2007 ARG seqType
Fri May 18 12:42:57 2007 ARG soCvsVersion 1.45
Fri May 18 12:42:57 2007 ARG sqlVerbose 0
Fri May 18 12:42:57 2007 ARG testNumber
Fri May 18 12:42:57 2007 ARG user
Fri May 18 12:42:57 2007 ARG verbose 1
Fri May 18 12:42:57 2007 ARG veryVerbose 0
Fri May 18 12:42:57 2007 AlgInvocationId 83
Fri May 18 12:42:57 2007 COMMIT commit off
Fri May 18 12:42:58 2007 Processing file
'/home/davila1/lguyanensis.gb'...
DBD::Pg::st execute failed: ERROR: duplicate key violates unique
constraint "pk_externaldatabase"
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.ExternalDatabase ( group_write, other_read,
group_read, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
Values: 1, 1, 1, HSSP, 1, 1, 18, 0, 83, 1, 1, 1 at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
'\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
'HASH(0x30d4870)') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 160
GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 134
GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 117
GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 106
GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 1021
GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 891
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 771
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 367
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HASH(0x2062a70)') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at
/system/GUS/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
/system/GUS/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
/system/GUS/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
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
STACK TRACE:
at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
'\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
'HASH(0x30d4870)') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 160
GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 134
GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 117
GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 106
GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 1021
GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 891
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 771
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 367
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HASH(0x2062a70)') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at
/system/GUS/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
/system/GUS/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
/system/GUS/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
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
This is my external_database table:
-- PostgreSQL database dump
--
SET client_encoding = 'UTF8';
SET standard_conforming_strings = off;
SET check_function_bodies = false;
SET client_min_messages = warning;
SET escape_string_warning = off;
SET search_path = sres, pg_catalog;
COPY externaldatabase (external_database_id, name, modification_date,
user_read, user_write, group_read, group_write, other_read, other_write,
row_user_id, row_group_id, row_project_id, row_alg_invocation_id) FROM
stdin;
164 RepBase 4.03 zebrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
106 maize-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2093 homstrad 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
89 mim 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1 assembly 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
154 RepBase 4.03 celrep.ref 4.0.4 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
82 mendel 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
185 RIKEN/FANTOM 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
292 Plasmodium_GSS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
102 hsc-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2096 PRODOM 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
189 COMPEL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3010 GeneDB_Lmajor 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2095 load 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
97 subtilist 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
90 mgd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
17 GSDB 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
92 aarhus/ghent-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
8 Brookhaven Protein Data Bank (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
184 ORNL GRAILExp gene predictions 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
12 GenPept 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
692 Plasmodium_TIGR 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
144 flybase translated orfs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3008 GeneDB_Afumigatus 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
165 RepBase 4.03 humsub.ref 1.0.2 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
13 IMAGE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
94 ecogene 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3024 GOA 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3011 GeneDB_Pberghei 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3018 GeneDB_Bpertussis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1392 CDD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3 EMBL Data Library (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2097 PFAMA 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
172 URL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
108 hiv 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
101 stygene 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3014 GeneDB_Tannulata 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
181 Signaling PAthway Database (SPAD) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
10 GenInfo Backbone Id (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2092 dbSNP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
78 embl 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
84 prosite 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3025 PubMed 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
6 Protein Research Foundation (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
928 GI 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
85 flybase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
14 EGAD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
126 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1792 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
156 RepBase 4.03 humrep.ref 7.0.6 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
152 TUBERCULIST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3005 GOC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
392 EPCon 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1892 PID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
98 eco2dbase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
104 transfac 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
293 Plasmodium_EST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
127 sptrembl 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
130 imgt/ligm 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1292 RATMAP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1192 ATCC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3001 GO Function 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
124 SWISS-PROT 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1494 CDD-Pfam 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
143 NCBI genomic Homo Sapiens 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
18 DOTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
133 estlib 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
161 RepBase 4.03 rodrep.ref 3.3.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
157 RepBase 4.03 invrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1495 CDD-Smart 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
79 pfam 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
103 carbbank 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
191 Whitehead Institute/MIT Center for Genome Research Mouse RH Map
2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
155 RepBase 4.03 drorep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
125 PSEUDO 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3006 GeneDB_Spombe 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3022 PMID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
153 RepBase 4.03 athrep.ref 4.0.5 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
122 SPTREMBL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
186 UCSC human draft genomic sequence (October 7 release) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
179 GeneMap 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
135 agis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3013 GeneDB_Pfalciparum 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
170 Pfam expert 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
178 StemCellDB public 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
149 Bucan lab. mouse BAC ends 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
148 Prodom 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3012 GeneDB_Pchabaudi 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
128 pseudo 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
175 INTERPRO 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
80 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3002 GO Component 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
21 gss_human_bak.seq 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1293 RGD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
9 Patents (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
15 BLOCKS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
37 swissprot 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2 GenBank (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
20 dbEST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
166 Demeter 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
5 NBRF PIR (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
81 pir 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
95 tigr 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1692 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
16 PRINTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
83 hssp 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3009 GeneDB_Ddiscoideum 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
163 RepBase 4.03 vrtrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3017 GeneDB_Bparapertussis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
87 wormpep 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
151 Plasmodium_RoosLab 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3016 GeneDB_Bbronchiseptica 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
146 S. cerevisiae translated orfs 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
182 UCSC human draft genomic sequence (June 15 release) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
4 DDBJ (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
159 RepBase 4.03 plnrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
105 zfin 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
190 TRRD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2094 cazy 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
22 GenBank 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
140 epd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3019 GeneDB_Styphi 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
145 C.elegans translated orfs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
162 RepBase 4.03 simple.ref 3.1 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
169 JGI/ORNL contigs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
88 dictydb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
173 SCOP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
793 Derisi Oligos 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
7 Swiss Prot (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3007 GeneDB_Scerevisiae 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
160 RepBase 4.03 pseudo.ref 1.0.5 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
91 swiss-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
129 imgt/hla 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
123 taxon 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
100 yepd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
96 sgd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1092 LocusID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
86 maizedb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
142 ORNL_grailexp_mrna 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
992 NCBI RefSeq 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3015 GeneDB_Tbrucei 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
147 TIGR mouse BAC ends 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
192 NCBI Malaria Genetics and Genome Project 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
99 gcrdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
11 General database Identifier (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
107 rebase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
180 KEGG: Kyoto Encyclopedia of Genes and Genomes 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3026 SWALL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
158 RepBase 4.03 mamrep.ref 5.2.2 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
492 Mouse BAC fingerprint map 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
177 Incyte 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
134 gdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
93 pdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3003 GO Process 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
167 Riethman lab. telomere sequences 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3021 SPTR 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
141 ORNL_genscan_mrna 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3023 TC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
174 SMART 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3020 GeneDB_Gmorsitans 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
139 rzpd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
168 NCBI Reference Sequence (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1294 COG 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1592 Schwartz Lab Optical Mapping Data 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
19 Unigene_44 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
183 ORNL GenScan gene predictions 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
171 Pfam-B 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
176 MEROPS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
150 Plasmodium_Sanger 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
\.
Thanks in advance for any help you might provide ;-)
Cheers, Alberto
davila wrote:
> 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) = @_;
> return unless $self->{bioperlSeqPreprocessor};
> my $class = $self->{bioperlSeqPreprocessor}->{class};
>
> eval {
> no strict "refs";
> eval "require $class";
> my $method = "${class}::preprocess";
> &$method($bioperlSeq); ### Line 63 originating the error #####
> };
>
> my $err = $@;
> if ($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
>
> 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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> ------------------------------------------------------------------------
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> _______________________________________________
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--
Alberto M. R. Dávila, PhD
Kinetoplastid Biology and Disease (Biomed Central)
http://www.kinetoplastids.com
IAEA Collaborating Center for Bioinformatics and Animal Genomics
DBBM / Instituto Oswaldo Cruz / FIOCRUZ
Av. Brasil 4365
Rio de Janeiro, RJ, Brasil
CEP 21040-900
Email: da...@fi...
amr...@gm...
Phone: 55-21-3865-8229 / 3865-8206
Fax: 55-21-2590-3495
-------------------------------------------------
The BiowebDB consortium: http://www.biowebdb.org
|
|
From: Mark S. H. <mh...@ug...> - 2007-05-18 14:30:11
|
Did you notice the requirements that you must "configure Tomcat to allow symlinks" for the webapp? On May 16, 2007, at 7:32 PM, mro...@cs... wrote: > Hello folks; > > We installed wdk, tomcat 6.0.10 and we are trying to get the > wdktoysite to > work. > > Everything compiled and all data files got create. > > Now when we try to start the site inside tomcat we get the > following errors: > > in catalina.log > May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start > SEVERE: Error listenerStart > May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start > SEVERE: Context [/wdktoysite] startup failed due to previous errors > > > in localhost.log > May 16, 2007 6:46:51 PM org.apache.catalina.core.StandardContext > listenerStart > SEVERE: Error configuring application listener of class > org.gusdb.wdk.controller.ApplicationInitListener > java.lang.ClassNotFoundException: > org.gusdb.wdk.controller.ApplicationInitListener > > and then all other errors have the same explanation > > java.lang.ClassNotFoundException: > org.gusdb.wdk.controller.ApplicationInitListener > > Has anybody run into this problem and how was it solved. > > > > Thanks > > Michael Robinson > Bioinformatics Research Group (Biorg) > Florida International University > ECS 254 > Miami, Florida, USA 33199 > > > > > > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Steve F. <sfi...@pc...> - 2007-05-17 23:52:47
|
hi michael- i suspect tomcat is not seeing your controller jar file. steve mro...@cs... wrote: > Hello folks; > > We installed wdk, tomcat 6.0.10 and we are trying to get the wdktoysite to > work. > > Everything compiled and all data files got create. > > Now when we try to start the site inside tomcat we get the following errors: > > in catalina.log > May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start > SEVERE: Error listenerSta > May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start > SEVERE: Context [/wdktoysite] startup failed due to previous errors > > > in localhost.log > May 16, 2007 6:46:51 PM org.apache.catalina.core.StandardContext > listenerStart > SEVERE: Error configuring application listener of class > org.gusdb.wdk.controller.ApplicationInitListener > java.lang.ClassNotFoundException: > org.gusdb.wdk.controller.ApplicationInitListener > > and then all other errors have the same explanation > > java.lang.ClassNotFoundException: > org.gusdb.wdk.controller.ApplicationInitListener > > Has anybody run into this problem and how was it solved. > > > > Thanks > > Michael Robinson > Bioinformatics Research Group (Biorg) > Florida International University > ECS 254 > Miami, Florida, USA 33199 > > > > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Steve F. <sfi...@pc...> - 2007-05-17 14:37:03
|
oops, indeed i had not added this file to SVN. i just did. it is in $PROJECT_HOME/GUS/Supported/lib/perl steve Alberto Davila wrote: > Dear John, > > Thanks for this ! > > I wonder this plugin "GUS::Supported::UnflattenBioperlFeatures" might > need to be loaded to the SVN site too ? I cannot find it ... > > Thanks and kind regards, Alberto > > > John Iodice wrote: > >> Alberto, >> >> Sorry, I forgot to check in those three plugins. They've now been added >> to the repository, so do an "svn update" and they'll be in >> Community/plugin/perl. >> >> John >> >> >> On May 7, 2007, at 3:37 PM, Alberto Davila wrote: >> >> >>> I really enjoyed to find this page: >>> >>> http://www.gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org >>> >>> but could not find these plugins : >>> >>> GUS::Community::Plugin::InsertInterproDomainDbs >>> >>> GUS::Community::Plugin::MakeGenesFromAlignments >>> >>> GUS::Community::Plugin::InsertInterproscanResults >>> >>> Where I should look for them ? >>> >>> Yet on the community plugins, trying to run this one got a version error: >>> >>> [user@localhost log]$ ga +create GUS::Community::Plugin::LoadPfam >>> FATAL: Database version does not match required version for Plugin. >>> Database Version: 3.5 Plugin Version: HASH(0x120e7b0) >>> >>> How should one debug this ? >>> >>> I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server. >>> >>> Thanks, Alberto >>> >>> > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Alberto D. <da...@io...> - 2007-05-17 11:51:01
|
Thanks Michael, I really loaded my taxon data first (exactly the same way you mention) , the problem appears to be related to a missing plugin... but of course I am not sure :-( Could you kindly check if you have "GUS::Supported::UnflattenBioperlFeatures" as part of GUS 3.5 ? Thanks mro...@cs... wrote: > Hi, > > i think i had the same error when i loaded my sequences, it was because i > had not loaded the taxon data first. > > This is how i loaded the taxon files: > > > Loading Taxons: 11-27-2006 by MR > > Data downloaded from: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz > > At: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy > > "The NCBI taxonomy database contains the names of all organisms that > are represented in the genetic databases with at least one nucleotide > or protein sequence. Click on the tree if you want to browse the > taxonomic structure or retrieve sequence data for a particular group of > organisms" > > > I used: http://www.gusdb.org/wiki/index.php/Bootstrap%20data as a guide, > THIS IS FOR GUSDB 3.0 VERSION, WE ARE USING VERISON 3.5. > > The instructions were corrected as follow: > > ga GUS::Supported::Plugin::LoadTaxon --gencode ~/taxon/11-27- > 2006/gencode.dmp --names ~/taxon/11-27-2006/names.dmp --nodes ~/taxon/11- > 27-2006/nodes.dmp --merged ~/taxon/11-27-2006/merged.dmp --commit > > > > For a manual loading to mySql see --> > http://linnaeus.zoology.gla.ac.uk/~rpage/iphylo/projects/3/ > > > Mon Nov 27 13:38:38 2006 Doing merge and NCBI tax id '413065' > not in database, skipping > Mon Nov 27 13:38:38 2006 Updating and inserting SRes.GeneticCode > > Mon Nov 27 13:53:12 2006 Processed ncbi_tax_id : 49833 > Mon Nov 27 13:53:12 2006 Processed ncbi_tax_id : 155113 > > Mon Nov 27 14:56:10 2006 Processed ncbi_tax_id : 83469 > Mon Nov 27 14:56:10 2006 Processed ncbi_tax_id : 195787 > > this is more clear: > ga GUS::Supported::Plugin::LoadTaxon > --gencode ~/taxon/11-27-2006/gencode.dmp > --names ~/taxon/11-27-2006/names.dmp > --nodes ~/taxon/11-27-2006/nodes.dmp > --merged ~/taxon/11-27-2006/merged.dmp --commit > > > > Hope it helps > > > Michael Robinson > Bioinformatics Research Group (Biorg) > Florida International University > ECS 254 > Miami, Florida, USA 33199 > > > > >> Send Gusdev-gusdev mailing list submissions to >> gus...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> or, via email, send a message with subject or body 'help' to >> gus...@li... >> >> You can reach the person managing the list at >> gus...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Gusdev-gusdev digest..." >> >> >> Today's Topics: >> >> 1. Re: ISF error (Steve Fischer) >> 2. RES: ISF error (davila) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 11 May 2007 14:01:47 -0400 >> From: Steve Fischer <sfi...@pc...> >> Subject: Re: [GUSDEV] ISF error >> To: davila <da...@io...> >> Cc: gus...@li..., mro...@cs..., >> cj...@fr... >> Message-ID: <464...@pc...> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> 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 >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Sat, 12 May 2007 13:35:16 -0300 >> From: "davila" <da...@io...> >> Subject: [GUSDEV] RES: ISF error >> To: "Steve Fischer" <sfi...@pc...> >> Cc: gus...@li..., mro...@cs..., >> pa...@ug..., Felipe Liberman <fl...@io...>, cj...@fr... >> Message-ID: >> <620...@be...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> 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) = @_; >> return unless $self->{bioperlSeqPreprocessor}; >> my $class = $self->{bioperlSeqPreprocessor}->{class}; >> >> eval { >> no strict "refs"; >> eval "require $class"; >> my $method = "${class}::preprocess"; >> &$method($bioperlSeq); ### Line 63 originating the error ##### >> }; >> >> my $err = $@; >> if ($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 >> >> 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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From: Alberto D. <da...@io...> - 2007-05-17 11:47:43
|
Dear John, Thanks for this ! I wonder this plugin "GUS::Supported::UnflattenBioperlFeatures" might need to be loaded to the SVN site too ? I cannot find it ... Thanks and kind regards, Alberto John Iodice wrote: > Alberto, > > Sorry, I forgot to check in those three plugins. They've now been added > to the repository, so do an "svn update" and they'll be in > Community/plugin/perl. > > John > > > On May 7, 2007, at 3:37 PM, Alberto Davila wrote: > >> I really enjoyed to find this page: >> >> http://www.gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org >> >> but could not find these plugins : >> >> GUS::Community::Plugin::InsertInterproDomainDbs >> >> GUS::Community::Plugin::MakeGenesFromAlignments >> >> GUS::Community::Plugin::InsertInterproscanResults >> >> Where I should look for them ? >> >> Yet on the community plugins, trying to run this one got a version error: >> >> [user@localhost log]$ ga +create GUS::Community::Plugin::LoadPfam >> FATAL: Database version does not match required version for Plugin. >> Database Version: 3.5 Plugin Version: HASH(0x120e7b0) >> >> How should one debug this ? >> >> I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server. >> >> Thanks, Alberto >> |
|
From: <mro...@cs...> - 2007-05-16 23:49:55
|
Hi, i think i had the same error when i loaded my sequences, it was because i had not loaded the taxon data first. This is how i loaded the taxon files: Loading Taxons: 11-27-2006 by MR Data downloaded from: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz At: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy "The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. Click on the tree if you want to browse the taxonomic structure or retrieve sequence data for a particular group of organisms" I used: http://www.gusdb.org/wiki/index.php/Bootstrap%20data as a guide, THIS IS FOR GUSDB 3.0 VERSION, WE ARE USING VERISON 3.5. The instructions were corrected as follow: ga GUS::Supported::Plugin::LoadTaxon --gencode ~/taxon/11-27- 2006/gencode.dmp --names ~/taxon/11-27-2006/names.dmp --nodes ~/taxon/11- 27-2006/nodes.dmp --merged ~/taxon/11-27-2006/merged.dmp --commit For a manual loading to mySql see --> http://linnaeus.zoology.gla.ac.uk/~rpage/iphylo/projects/3/ Mon Nov 27 13:38:38 2006 Doing merge and NCBI tax id '413065' not in database, skipping Mon Nov 27 13:38:38 2006 Updating and inserting SRes.GeneticCode Mon Nov 27 13:53:12 2006 Processed ncbi_tax_id : 49833 Mon Nov 27 13:53:12 2006 Processed ncbi_tax_id : 155113 Mon Nov 27 14:56:10 2006 Processed ncbi_tax_id : 83469 Mon Nov 27 14:56:10 2006 Processed ncbi_tax_id : 195787 this is more clear: ga GUS::Supported::Plugin::LoadTaxon --gencode ~/taxon/11-27-2006/gencode.dmp --names ~/taxon/11-27-2006/names.dmp --nodes ~/taxon/11-27-2006/nodes.dmp --merged ~/taxon/11-27-2006/merged.dmp --commit Hope it helps Michael Robinson Bioinformatics Research Group (Biorg) Florida International University ECS 254 Miami, Florida, USA 33199 > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gusdev-gusdev digest..." > > > Today's Topics: > > 1. Re: ISF error (Steve Fischer) > 2. RES: ISF error (davila) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 May 2007 14:01:47 -0400 > From: Steve Fischer <sfi...@pc...> > Subject: Re: [GUSDEV] ISF error > To: davila <da...@io...> > Cc: gus...@li..., mro...@cs..., > cj...@fr... > Message-ID: <464...@pc...> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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 >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------ > > Message: 2 > Date: Sat, 12 May 2007 13:35:16 -0300 > From: "davila" <da...@io...> > Subject: [GUSDEV] RES: ISF error > To: "Steve Fischer" <sfi...@pc...> > Cc: gus...@li..., mro...@cs..., > pa...@ug..., Felipe Liberman <fl...@io...>, cj...@fr... > Message-ID: > <620...@be...> > Content-Type: text/plain; charset="iso-8859-1" > > 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) = @_; > return unless $self->{bioperlSeqPreprocessor}; > my $class = $self->{bioperlSeqPreprocessor}->{class}; > > eval { > no strict "refs"; > eval "require $class"; > my $method = "${class}::preprocess"; > &$method($bioperlSeq); ### Line 63 originating the error ##### > }; > > my $err = $@; > if ($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 > > 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 >> > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest, Vol 11, Issue 4 > ******************************************** > |
|
From: <mro...@cs...> - 2007-05-16 23:32:53
|
Hello folks;
We installed wdk, tomcat 6.0.10 and we are trying to get the wdktoysite to
work.
Everything compiled and all data files got create.
Now when we try to start the site inside tomcat we get the following errors:
in catalina.log
May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
May 16, 2007 7:06:44 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/wdktoysite] startup failed due to previous errors
in localhost.log
May 16, 2007 6:46:51 PM org.apache.catalina.core.StandardContext
listenerStart
SEVERE: Error configuring application listener of class
org.gusdb.wdk.controller.ApplicationInitListener
java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener
and then all other errors have the same explanation
java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener
Has anybody run into this problem and how was it solved.
Thanks
Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
ECS 254
Miami, Florida, USA 33199
|
|
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
>
|
|
From: Steve F. <sfi...@pc...> - 2007-05-11 18:02:05
|
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
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: davila <da...@io...> - 2007-05-11 17:36:07
|
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=3Dmydb
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::Supp=
orted::Plugin::InsertSequenceFeatures=3DHASH(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::Supporte=
d::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)') called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
645
=
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS:=
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
604
=
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
574
=
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Sup=
ported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
361
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(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=3DHASH(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::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(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=3Dmydb
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:
=20
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::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(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=3DHASH(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::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(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::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(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=3DHASH(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::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(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=20
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=20
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","mod=
ification_date","row_project_id","row_alg_invocation_id" FROM =
"sres"."taxonname" WHERE=20
"name" =3D 'Leishmania guyanensis';
taxon_name_id | taxon_id | name | unique_name_variant =
| name_class | modification_date | row_project_id | =
row_alg_invocation_id=20
---------------+----------+-----------------------+---------------------+=
-----------------+---------------------------+----------------+----------=
-------------
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
|
|
From: John I. <io...@pc...> - 2007-05-08 02:21:26
|
Alberto, Sorry, I forgot to check in those three plugins. They've now been added to the repository, so do an "svn update" and they'll be in Community/plugin/perl. John On May 7, 2007, at 3:37 PM, Alberto Davila wrote: > I really enjoyed to find this page: > > http://www.gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org > > but could not find these plugins : > > GUS::Community::Plugin::InsertInterproDomainDbs > > GUS::Community::Plugin::MakeGenesFromAlignments > > GUS::Community::Plugin::InsertInterproscanResults > > Where I should look for them ? > > Yet on the community plugins, trying to run this one got a version > error: > > [user@localhost log]$ ga +create GUS::Community::Plugin::LoadPfam > FATAL: Database version does not match required version for Plugin. > Database Version: 3.5 Plugin Version: HASH(0x120e7b0) > > How should one debug this ? > > I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server. > > Thanks, Alberto > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Alberto D. <da...@io...> - 2007-05-07 19:42:29
|
I really enjoyed to find this page: http://www.gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org but could not find these plugins : GUS::Community::Plugin::InsertInterproDomainDbs GUS::Community::Plugin::MakeGenesFromAlignments GUS::Community::Plugin::InsertInterproscanResults Where I should look for them ? Yet on the community plugins, trying to run this one got a version error: [user@localhost log]$ ga +create GUS::Community::Plugin::LoadPfam FATAL: Database version does not match required version for Plugin. Database Version: 3.5 Plugin Version: HASH(0x120e7b0) How should one debug this ? I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server. Thanks, Alberto |
|
From: Alberto D. <da...@io...> - 2007-05-07 19:32:44
|
Thanks Mark ! Yet on ontologies, I just realized there is no "LoadGoOntology" plugin in GUS 3.5 (http://www.gusdb.org/wiki/index.php/Bootstrap%20data#GOOntolgy), anyway trying to use "GUS::Supported::Plugin::InsertGeneOntology" I got the following errors: [user@localhost log]$ ga GUS::Supported::Plugin::InsertGeneOntology --flatFile function.ontology --filePath /home/user/GO/ --functionExtDbName function --createRelease 1.12 Mon May 7 16:17:39 2007 DSN dbi:Pg:dbname=mydb Mon May 7 16:17:39 2007 PLUGIN GUS::Supported::Plugin::InsertGeneOntology Mon May 7 16:17:39 2007 ARG algoinvo 1 Mon May 7 16:17:39 2007 ARG comment Mon May 7 16:17:39 2007 ARG commit 0 Mon May 7 16:17:39 2007 ARG componentExtDbName Mon May 7 16:17:39 2007 ARG createRelease 1 Mon May 7 16:17:39 2007 ARG debug 0 Mon May 7 16:17:39 2007 ARG filePath /home/user/GO/ Mon May 7 16:17:39 2007 ARG flatFile function.ontology Mon May 7 16:17:39 2007 ARG functionExtDbName function Mon May 7 16:17:39 2007 ARG group Mon May 7 16:17:39 2007 ARG gusconfigfile $GUS_HOME/config/gus.config Mon May 7 16:17:39 2007 ARG help Mon May 7 16:17:39 2007 ARG helpHTML Mon May 7 16:17:39 2007 ARG loadAgain 0 Mon May 7 16:17:39 2007 ARG processExtDbName Mon May 7 16:17:39 2007 ARG project Mon May 7 16:17:39 2007 ARG sqlVerbose 0 Mon May 7 16:17:39 2007 ARG user Mon May 7 16:17:39 2007 ARG verbose 0 Mon May 7 16:17:39 2007 ARG veryVerbose 0 Mon May 7 16:17:39 2007 AlgInvocationId 36 Mon May 7 16:17:39 2007 COMMIT commit off Mon May 7 16:17:39 2007 loading function.ontology in preparation for parsing Mon May 7 16:17:39 2007 parsing all .ontology files in preparation for inserting into database Mon May 7 16:17:40 2007 parsing finished; loading ontology into database ERROR: USER ERROR: Couldn't find external database function. Use the plugin InsertExternalDatabase to insert this information into the database. STACK TRACE: at /usr/lib/perl5/site_perl/5.8.8/Error.pm line 189 Error::throw('GUS::PluginMgr::PluginUserError=HASH(0x1519d50)') called at $GUS_HOME/lib/perl/GUS/PluginMgr/Plugin.pm line 1226 GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 'Couldn\'t find external database function. Use the plugin Ins...') called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm line 490 GUS::Supported::Plugin::InsertGeneOntology::getExtDbRelId('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 'function', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x12402c0)') called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm line 222 GUS::Supported::Plugin::InsertGeneOntology::loadOntology('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x1432670)') called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm line 166 GUS::Supported::Plugin::InsertGeneOntology::run('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 'HASH(0x14327d0)') 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::InsertGeneOntology', 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::InsertGeneOntology') called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 'GUS::Supported::Plugin::InsertGeneOntology') 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 $GUS_HOME/bin/ga line 11 This is the function.ontology file I was trying to load: ftp://ftp.geneontology.org/pub/go/ontology/function.ontology And when trying to create the external-database I got this error: [user@localhost log]$ ga GUS::Supported::Plugin::InsertExternalDatabase --name function.ontology --verbose Mon May 7 16:24:19 2007 DSN dbi:Pg:dbname=mydb Mon May 7 16:24:19 2007 PLUGIN GUS::Supported::Plugin::InsertExternalDatabase Mon May 7 16:24:19 2007 ARG algoinvo 1 Mon May 7 16:24:19 2007 ARG comment Mon May 7 16:24:19 2007 ARG commit 0 Mon May 7 16:24:19 2007 ARG debug 0 Mon May 7 16:24:19 2007 ARG group Mon May 7 16:24:19 2007 ARG gusconfigfile $GUS_HOME/config/gus.config Mon May 7 16:24:19 2007 ARG help Mon May 7 16:24:19 2007 ARG helpHTML Mon May 7 16:24:19 2007 ARG name function.ontology Mon May 7 16:24:19 2007 ARG project Mon May 7 16:24:19 2007 ARG sqlVerbose 0 Mon May 7 16:24:19 2007 ARG user Mon May 7 16:24:19 2007 ARG verbose 1 Mon May 7 16:24:19 2007 ARG veryVerbose 0 Mon May 7 16:24:19 2007 AlgInvocationId 37 Mon May 7 16:24:19 2007 COMMIT commit off DBD::Pg::st execute failed: ERROR: duplicate key violates unique constraint "pk_externaldatabase" ERROR: SQL ERROR!! involving INSERT INTO SRes.ExternalDatabase ( group_write, other_read, group_read, name, user_read, row_user_id, external_database_id, modification_date, other_write, row_alg_invocation_id, row_project_id, row_group_id, user_write ) VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? ) Values: 1, 1, 1, function.ontology, 1, 1, 7, 0, 37, 1, 1, 1 at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO SRes.ExternalDataba...') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x13c8a80)', 'ARRAY(0x13c8b50)', '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 673 GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)', 'HASH(0x13b1df0)') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 620 GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') called at $GUS_HOME/lib/perl/GUS/Model/GusRow.pm line 1692 GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertExternalDatabase.pm line 103 GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported::Plugin::InsertExternalDatabase=HASH(0xf7eeb0)', 'HASH(0x12eca80)') 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::InsertExternalDatabase', 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::InsertExternalDatabase') called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 'GUS::Supported::Plugin::InsertExternalDatabase') 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/ObjRelP/DbiDbHandle.pm line 166 GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO SRes.ExternalDataba...') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x13c8a80)', 'ARRAY(0x13c8b50)', '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 673 GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)', 'HASH(0x13b1df0)') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 620 GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') called at $GUS_HOME/lib/perl/GUS/Model/GusRow.pm line 1692 GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertExternalDatabase.pm line 103 GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported::Plugin::InsertExternalDatabase=HASH(0xf7eeb0)', 'HASH(0x12eca80)') called at /$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::InsertExternalDatabase', 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::InsertExternalDatabase') called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 'GUS::Supported::Plugin::InsertExternalDatabase') 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 I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server. Thanks, Alberto Mark S. Heiges wrote: > That plugin requires the file in OBO format. You can download the latest > from the SO Project's repository at > http://song.cvs.sourceforge.net/song/ontology/so.obo > > You can safely ignore the "no 'undoTables()'" message. It just indicates > that InsertSequenceOntologyOBO has not implemented some optional record > keeping and, as a side effect, is not compatible with the > GUS::Community::Plugin::Undo plugin. The "RESULT Inserted n terms into > SequenceOntology" message will give an accurate count of what was loaded. > > > On May 5, 2007, at 11:04 AM, davila wrote: > >> Hi folks, >> >> With GUS 3.5 got from SVN, tryig to use the >> GUS::Supported::Plugin::InsertSequenceOntologyOBO plugin I got no rows >> inserted, see the log: >> >> GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile >> so.definition --soCvsVersion '1.42' --soVersion >> '1.419' --user user --group group --commit >so1.log >> >> Sat May 5 11:41:22 2007 DSN dbi:Pg:dbname=mydb >> Sat May 5 11:41:22 2007 PLUGIN >> GUS::Supported::Plugin::InsertSequenceOntologyOBO >> Sat May 5 11:41:22 2007 ARG algoinvo 1 >> Sat May 5 11:41:22 2007 ARG comment >> Sat May 5 11:41:22 2007 ARG commit 1 >> Sat May 5 11:41:22 2007 ARG debug 0 >> Sat May 5 11:41:22 2007 ARG group dba >> Sat May 5 11:41:22 2007 ARG gusconfigfile >> $GUS_HOME/gus.config >> Sat May 5 11:41:22 2007 ARG help >> Sat May 5 11:41:22 2007 ARG helpHTML >> Sat May 5 11:41:22 2007 ARG inputFile so.definition >> Sat May 5 11:41:22 2007 ARG project >> Sat May 5 11:41:22 2007 ARG soCvsVersion 1.42 >> Sat May 5 11:41:22 2007 ARG soVersion 1.419 >> Sat May 5 11:41:22 2007 ARG sqlVerbose 0 >> Sat May 5 11:41:22 2007 ARG user dba >> Sat May 5 11:41:22 2007 ARG verbose 0 >> Sat May 5 11:41:22 2007 ARG veryVerbose 0 >> Sat May 5 11:41:22 2007 AlgInvocationId 14 >> Sat May 5 11:41:22 2007 COMMIT commit on >> Sat May 5 11:41:22 2007 TIME < 1 sec (0:00:00) >> Sat May 5 11:41:22 2007 RESULT Inserted 0 terms into >> SequenceOntology >> Sat May 5 11:41:22 2007 Rows Written N/A (plugin has no >> 'undoTables()' method) >> Sat May 5 11:41:22 2007 AlgInvocationId 14 >> Sat May 5 11:41:22 2007 COMMIT commit on >> >> >> What exactly means this warining "Rows Written N/A (plugin has no >> 'undoTables()' method)" ? >> >> and where one can find and download the most updated "so.definitions" >> file ? >> >> >> My sres.gorelationship and sres.sequenceontology are like this: >> >> >> mydb=# \d sres.gorelationship >> Table "sres.gorelationship" >> Column | Type | Modifiers >> -------------------------+-----------------------------+----------- >> go_relationship_id | numeric(10,0) | not null >> parent_term_id | numeric(10,0) | not null >> child_term_id | numeric(10,0) | not null >> go_relationship_type_id | numeric(10,0) | not null >> modification_date | timestamp without time zone | not null >> user_read | numeric(1,0) | not null >> user_write | numeric(1,0) | not null >> group_read | numeric(1,0) | not null >> group_write | numeric(1,0) | not null >> other_read | numeric(1,0) | not null >> other_write | numeric(1,0) | not null >> row_user_id | numeric(12,0) | not null >> row_group_id | numeric(4,0) | not null >> row_project_id | numeric(4,0) | not null >> row_alg_invocation_id | numeric(12,0) | not null >> Indexes: >> "gorelationship_pk" PRIMARY KEY, btree (go_relationship_id) >> "gorelationship_ind01" btree (parent_term_id, child_term_id) >> "gorelationship_ind02" btree (child_term_id, parent_term_id) >> "gorelationship_ind03" btree (go_relationship_type_id) >> >> >> mydb=# \d sres.sequenceontology >> Table "sres.sequenceontology" >> Column | Type | Modifiers >> -----------------------+-----------------------------+----------- >> sequence_ontology_id | numeric(10,0) | not null >> so_id | character varying(12) | not null >> ontology_name | character varying(30) | not null >> so_version | character varying(255) | not null >> so_cvs_version | character varying(10) | not null >> term_name | character varying(255) | not null >> definition | character varying(2000) | not null >> modification_date | timestamp without time zone | not null >> user_read | numeric(1,0) | not null >> user_write | numeric(1,0) | not null >> group_read | numeric(1,0) | not null >> group_write | numeric(1,0) | not null >> other_read | numeric(1,0) | not null >> other_write | numeric(1,0) | not null >> row_user_id | numeric(12,0) | not null >> row_group_id | numeric(4,0) | not null >> row_project_id | numeric(4,0) | not null >> row_alg_invocation_id | numeric(12,0) | not null >> Indexes: >> "pk_sequenceontology" PRIMARY KEY, btree (sequence_ontology_id) >> >> Thanks, Alberto >> |
|
From: Mark S. H. <mh...@ug...> - 2007-05-05 18:31:27
|
That plugin requires the file in OBO format. You can download the latest from the SO Project's repository at http://song.cvs.sourceforge.net/song/ontology/so.obo You can safely ignore the "no 'undoTables()'" message. It just indicates that InsertSequenceOntologyOBO has not implemented some optional record keeping and, as a side effect, is not compatible with the GUS::Community::Plugin::Undo plugin. The "RESULT Inserted n terms into SequenceOntology" message will give an accurate count of what was loaded. On May 5, 2007, at 11:04 AM, davila wrote: > Hi folks, > > With GUS 3.5 got from SVN, tryig to use the > GUS::Supported::Plugin::InsertSequenceOntologyOBO plugin I got no > rows inserted, see the log: > > GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile > so.definition --soCvsVersion '1.42' --soVersion > '1.419' --user user --group group --commit >so1.log > > Sat May 5 11:41:22 2007 DSN dbi:Pg:dbname=mydb > Sat May 5 11:41:22 2007 PLUGIN > GUS::Supported::Plugin::InsertSequenceOntologyOBO > Sat May 5 11:41:22 2007 ARG algoinvo 1 > Sat May 5 11:41:22 2007 ARG comment > Sat May 5 11:41:22 2007 ARG commit 1 > Sat May 5 11:41:22 2007 ARG debug 0 > Sat May 5 11:41:22 2007 ARG group dba > Sat May 5 11:41:22 2007 ARG gusconfigfile $GUS_HOME/ > gus.config > Sat May 5 11:41:22 2007 ARG help > Sat May 5 11:41:22 2007 ARG helpHTML > Sat May 5 11:41:22 2007 ARG inputFile so.definition > Sat May 5 11:41:22 2007 ARG project > Sat May 5 11:41:22 2007 ARG soCvsVersion 1.42 > Sat May 5 11:41:22 2007 ARG soVersion 1.419 > Sat May 5 11:41:22 2007 ARG sqlVerbose 0 > Sat May 5 11:41:22 2007 ARG user dba > Sat May 5 11:41:22 2007 ARG verbose 0 > Sat May 5 11:41:22 2007 ARG veryVerbose 0 > Sat May 5 11:41:22 2007 AlgInvocationId 14 > Sat May 5 11:41:22 2007 COMMIT commit on > Sat May 5 11:41:22 2007 TIME < 1 sec (0:00:00) > Sat May 5 11:41:22 2007 RESULT Inserted 0 terms into > SequenceOntology > Sat May 5 11:41:22 2007 Rows Written N/A (plugin has no > 'undoTables()' method) > Sat May 5 11:41:22 2007 AlgInvocationId 14 > Sat May 5 11:41:22 2007 COMMIT commit on > > > What exactly means this warining "Rows Written N/A (plugin has > no 'undoTables()' method)" ? > > and where one can find and download the most updated > "so.definitions" file ? > > > My sres.gorelationship and sres.sequenceontology are like this: > > > mydb=# \d sres.gorelationship > Table "sres.gorelationship" > Column | Type | Modifiers > -------------------------+-----------------------------+----------- > go_relationship_id | numeric(10,0) | not null > parent_term_id | numeric(10,0) | not null > child_term_id | numeric(10,0) | not null > go_relationship_type_id | numeric(10,0) | not null > modification_date | timestamp without time zone | not null > user_read | numeric(1,0) | not null > user_write | numeric(1,0) | not null > group_read | numeric(1,0) | not null > group_write | numeric(1,0) | not null > other_read | numeric(1,0) | not null > other_write | numeric(1,0) | not null > row_user_id | numeric(12,0) | not null > row_group_id | numeric(4,0) | not null > row_project_id | numeric(4,0) | not null > row_alg_invocation_id | numeric(12,0) | not null > Indexes: > "gorelationship_pk" PRIMARY KEY, btree (go_relationship_id) > "gorelationship_ind01" btree (parent_term_id, child_term_id) > "gorelationship_ind02" btree (child_term_id, parent_term_id) > "gorelationship_ind03" btree (go_relationship_type_id) > > > mydb=# \d sres.sequenceontology > Table "sres.sequenceontology" > Column | Type | Modifiers > -----------------------+-----------------------------+----------- > sequence_ontology_id | numeric(10,0) | not null > so_id | character varying(12) | not null > ontology_name | character varying(30) | not null > so_version | character varying(255) | not null > so_cvs_version | character varying(10) | not null > term_name | character varying(255) | not null > definition | character varying(2000) | not null > modification_date | timestamp without time zone | not null > user_read | numeric(1,0) | not null > user_write | numeric(1,0) | not null > group_read | numeric(1,0) | not null > group_write | numeric(1,0) | not null > other_read | numeric(1,0) | not null > other_write | numeric(1,0) | not null > row_user_id | numeric(12,0) | not null > row_group_id | numeric(4,0) | not null > row_project_id | numeric(4,0) | not null > row_alg_invocation_id | numeric(12,0) | not null > Indexes: > "pk_sequenceontology" PRIMARY KEY, btree (sequence_ontology_id) > > Thanks, Alberto > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: davila <da...@io...> - 2007-05-05 15:10:17
|
Hi folks,
With GUS 3.5 got from SVN, tryig to use the =
GUS::Supported::Plugin::InsertSequenceOntologyOBO plugin I got no rows =
inserted, see the log:
GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile =
so.definition --soCvsVersion '1.42' --soVersion
'1.419' --user user --group group --commit >so1.log
Sat May 5 11:41:22 2007 DSN dbi:Pg:dbname=3Dmydb
Sat May 5 11:41:22 2007 PLUGIN
GUS::Supported::Plugin::InsertSequenceOntologyOBO
Sat May 5 11:41:22 2007 ARG algoinvo 1
Sat May 5 11:41:22 2007 ARG comment
Sat May 5 11:41:22 2007 ARG commit 1
Sat May 5 11:41:22 2007 ARG debug 0
Sat May 5 11:41:22 2007 ARG group dba
Sat May 5 11:41:22 2007 ARG gusconfigfile =
$GUS_HOME/gus.config
Sat May 5 11:41:22 2007 ARG help
Sat May 5 11:41:22 2007 ARG helpHTML
Sat May 5 11:41:22 2007 ARG inputFile so.definition
Sat May 5 11:41:22 2007 ARG project
Sat May 5 11:41:22 2007 ARG soCvsVersion 1.42
Sat May 5 11:41:22 2007 ARG soVersion 1.419
Sat May 5 11:41:22 2007 ARG sqlVerbose 0
Sat May 5 11:41:22 2007 ARG user dba
Sat May 5 11:41:22 2007 ARG verbose 0
Sat May 5 11:41:22 2007 ARG veryVerbose 0
Sat May 5 11:41:22 2007 AlgInvocationId 14
Sat May 5 11:41:22 2007 COMMIT commit on
Sat May 5 11:41:22 2007 TIME < 1 sec (0:00:00)
Sat May 5 11:41:22 2007 RESULT Inserted 0 terms into
SequenceOntology
Sat May 5 11:41:22 2007 Rows Written N/A (plugin has no
'undoTables()' method)
Sat May 5 11:41:22 2007 AlgInvocationId 14
Sat May 5 11:41:22 2007 COMMIT commit on
What exactly means this warining "Rows Written N/A (plugin has no =
'undoTables()' method)" ?
and where one can find and download the most updated "so.definitions" =
file ?
My sres.gorelationship and sres.sequenceontology are like this:
mydb=3D# \d sres.gorelationship
Table "sres.gorelationship"
Column | Type | Modifiers
-------------------------+-----------------------------+-----------
go_relationship_id | numeric(10,0) | not null
parent_term_id | numeric(10,0) | not null
child_term_id | numeric(10,0) | not null
go_relationship_type_id | numeric(10,0) | not null
modification_date | timestamp without time zone | not null
user_read | numeric(1,0) | not null
user_write | numeric(1,0) | not null
group_read | numeric(1,0) | not null
group_write | numeric(1,0) | not null
other_read | numeric(1,0) | not null
other_write | numeric(1,0) | not null
row_user_id | numeric(12,0) | not null
row_group_id | numeric(4,0) | not null
row_project_id | numeric(4,0) | not null
row_alg_invocation_id | numeric(12,0) | not null
Indexes:
"gorelationship_pk" PRIMARY KEY, btree (go_relationship_id)
"gorelationship_ind01" btree (parent_term_id, child_term_id)
"gorelationship_ind02" btree (child_term_id, parent_term_id)
"gorelationship_ind03" btree (go_relationship_type_id)
mydb=3D# \d sres.sequenceontology
Table "sres.sequenceontology"
Column | Type | Modifiers
-----------------------+-----------------------------+-----------
sequence_ontology_id | numeric(10,0) | not null
so_id | character varying(12) | not null
ontology_name | character varying(30) | not null
so_version | character varying(255) | not null
so_cvs_version | character varying(10) | not null
term_name | character varying(255) | not null
definition | character varying(2000) | not null
modification_date | timestamp without time zone | not null
user_read | numeric(1,0) | not null
user_write | numeric(1,0) | not null
group_read | numeric(1,0) | not null
group_write | numeric(1,0) | not null
other_read | numeric(1,0) | not null
other_write | numeric(1,0) | not null
row_user_id | numeric(12,0) | not null
row_group_id | numeric(4,0) | not null
row_project_id | numeric(4,0) | not null
row_alg_invocation_id | numeric(12,0) | not null
Indexes:
"pk_sequenceontology" PRIMARY KEY, btree (sequence_ontology_id)
Thanks, Alberto
|
|
From: Alberto D. <da...@io...> - 2007-05-04 17:23:00
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Hi folks, In a fresh install of GUS 3.5 in an AMD64 server, we realized there is some info missing in the gus.config file, the original one downloaded from SVN is like this: http://www.biowebdb.org/wiki/index.php/%24PROJECT_HOME/install/gus.config.sample When we run: ga +meta --commit got this error: FATAL: Database version does not match required version for Plugin. Database Version: Plugin Version: 3.5 Our guys solved this by adding "3.5" directly in the plugin then it is inserted in the core.databaseversion table... but this is obviously not the best solution... I vaguely remember there was a variable in "gus.config" stating the GUS version (eg: 3.5) but it does not exist in the current "gus.config" version. Cheers, Alberto |
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From: Chris S. <sto...@pc...> - 2007-03-07 02:55:31
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Brian, Sorry to have not responded earlier to this. Basically I agree. A superclass should maintain the semantics of having attributes common to all. This means we either have to only use named attributes for those common attributes or to allow named attributes for foreign keys that are not in the superclass and I agree with your recommendation to go with the latter (allow named attributes not in superclass so that foreign keys can be included as needed), Cheers, Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu On Feb 7, 2007, at 5:02 PM, Brian Brunk wrote: > I would like to raise for discussion an issue that we have been > faced with here at Penn in the last couple of weeks. It turns out > that in GUS3.5 all named attributes of imp tables are now included > in the superclass view. Following is the aafeature view: > > > column nulls? type > AA_Feature_ID no NUMBER(10,0) > AA_SEQUENCE_ID no DoTS::AASequence (NUMBER(10,0) ) > Feature_NAME_ID DoTS::FeatureName (NUMBER(10,0) ) > PARENT_ID DoTS::AAFeature (NUMBER(10,0) ) > NA_Feature_ID DoTS::NAFeature (NUMBER(10,0) ) > SUBCLASS_VIEW STRING(30) > SEQUENCE_ONTOLOGY_ID SRes::SequenceOntology (NUMBER(10,0) ) > DESCRIPTION STRING(4000) > PFAM_ENTRY_ID DoTS::PfamEntry (NUMBER(10,0) ) > MOTIF_AA_SEQUENCE_ID DoTS::AASequence (NUMBER(10,0) ) > REPEAT_TYPE_ID DoTS::RepeatType (NUMBER(10,0) ) > EXTERNAL_DATABASE_RELEASE_ID SRes::ExternalDatabaseRelease (NUMBER > (10,0) ) > SOURCE_ID STRING(50) > PREDICTION_ALGORITHM_ID Core::Algorithm (NUMBER(5,0) ) > IS_PREDICTED no NUMBER(1,0) > REVIEW_STATUS_ID SRes::ReviewStatus (NUMBER(12,0) ) > MODIFICATION_DATE no DATE > > My understanding of the intent of superclass views is that they > have attributes that are common to all subclasses in a typical > class hierarchy. From a biological perspective, this would be > attributes that are common to all (or at least nearly all) > features. Because all named attributes are now in this view, there > are a number of attributes that are not relevant for all aafeatures > (or even the majority of aafeatures). This is because GUS also has > a requirement that all fields used in foreign key references must > be named attributes. This is for clarity and makes obvious sense. > This means, however, that now these foreign key attributes are > included in the superclass view (and inherited by all the > subclasses). The above table has three such attributes that I > think would be much better served only in the specific views that > need them such as DoTS::RepeatRegionAAFeature for repeat_type_id. > I don't see any views where it is obvious to me one would want to > use pfam_entry_id or motif_aa_sequence_id. > > PFAM_ENTRY_ID DoTS::PfamEntry (NUMBER(10,0) ) > MOTIF_AA_SEQUENCE_ID DoTS::AASequence (NUMBER(10,0) ) > REPEAT_TYPE_ID DoTS::RepeatType (NUMBER(10,0) ) > > The motif_aa_sequence_id is particularly problematic as this causes > there to be two foreign key references into the aasequence table. > The PERL object layer only supports having two foreign key > references to a table via manual entries into the special cases > file. This works fine for a limited number of tables (views) but > is overwhelming when dealing with a large number such as for all > the aafeature views. > > I would propose that we drop these extra named attributes from the > superclass views in the next release of GUS. This will clean up > all the views and make them easier to understand. It will also > alleviate problems with the PERL object layer related to multiple > foreign key references. For those views that contain multiple > references such as RepeatRegionAAFeature, we should enter the > necessary lines in the special_cases file so that the objects work > without coding around the limitation (which is what I suspect > persons are doing now). > > Comments? > > -Brian > > Brian P. Brunk, Ph.D. > ApiDB Senior Manager > 1424 Blockley Hall > Penn Center For Bioinformatics > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3118 > Fax: 215-573-3111 > > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642______________________________ > _________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Bindu G. <bi...@pc...> - 2007-03-02 21:54:39
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string1 in VirtualSequence is 'confidence', which Toxo is not using. it should be pretty straightforward to flip this with string2 (source_id). Bindu On Mar 2, 2007, at 4:19 PM, Steve Fischer wrote: > ok, great. > > no, source_id is string1 in one view and string2. we'd have to > adjust that. > > in Api we plan on correcting this with a schema/data patch. > > steve > > pi...@pc... wrote: > >> I agree with this. In fact, the current database being used by our >> mammalian >> DoTS build has incorporated a source_id into the assembly view of >> NASequence. I >> believe (could be wrong on this) that this is the only view without a >> source_id. So this would clear the way to having source_id in the >> super class >> for the "official" GUS schema. Are all the nasequenceimp views >> using the same >> field for source_id? Are there other views missing a source_id? >> >> >> >> >> Quoting Steve Fischer <sfi...@pc...>: >> >> >> >>> folks- >>> >>> we've been again reminded of the issue that toxo stores its >>> chromosome >>> sequence in VirtualSequence while the other two use >>> ExternalNaSequence. >>> >>> this means that we cannot re-use sql code, which is a headache. >>> >>> our proposed solution is to upgrade NaSequence view (the >>> superclass) to >>> have a source_id column. We feel that this is correct >>> semantically, >>> and also solves our problem. >>> >>> the semantics are that: >>> (1) NaSequence already has an external_database_release_id, which >>> makes no sense w/o source_id >>> (2) the pair (external_database_release_id, source_id) has >>> "universal" >>> semantics (ie, not just limited to "external" sequences). that >>> semantics is "dataset and stable_id" >>> >>> steve >>> _______________________________________________ >>> ApiDB mailing list >>> Ap...@pc... >>> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb >>> >>> >>> >> >> >> >> >> --------------------------------------------------------------------- >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > _______________________________________________ > ApiDB mailing list > Ap...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/apidb |
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From: Frank I. <inn...@pc...> - 2007-03-02 21:51:45
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Over the next few weeks I will be reviewing the amendments that been submitted to our change management tracker, as well as the changes made less formally to instances of GUS 3.5 installs within our own lab. We are also seeking input from other GUS users, to review what changes they have made to their base GUS 3.5 installations. If you have any changes or additions that you would like to also be considered for the next release, please email me with your suggestions. Thanks. -Frank Frank Innamorato Database Administrator Computational Biology and Informatics Laboratory Penn Center for Bioinformatics 1410 Blockley Hall 423 Guardian Drive University of Pennsylvania Philadelphia, PA 19104 Chris Stoeckert wrote: > As I mentioned in another gusdev mail thread, I would like (Frank) to > generate a list of proposed changes to incorporate into a GUS 3.6 > release hopefully sometime this month. If those on the gusdev list > agree then sometime next month we will start assigning changes for > supported plug ins. > > Chris > |
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From: Chris S. <sto...@pc...> - 2007-03-02 21:28:12
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As I mentioned in another gusdev mail thread, I would like (Frank) to generate a list of proposed changes to incorporate into a GUS 3.6 release hopefully sometime this month. If those on the gusdev list agree then sometime next month we will start assigning changes for supported plug ins. Chris On Mar 2, 2007, at 4:19 PM, Steve Fischer wrote: > ok, great. > > no, source_id is string1 in one view and string2. we'd have to > adjust that. > > in Api we plan on correcting this with a schema/data patch. > > steve > > pi...@pc... wrote: > >> I agree with this. In fact, the current database being used by our >> mammalian >> DoTS build has incorporated a source_id into the assembly view of >> NASequence. I >> believe (could be wrong on this) that this is the only view without a >> source_id. So this would clear the way to having source_id in the >> super class >> for the "official" GUS schema. Are all the nasequenceimp views >> using the same >> field for source_id? Are there other views missing a source_id? >> >> >> >> >> Quoting Steve Fischer <sfi...@pc...>: >> >> >> >>> folks- >>> >>> we've been again reminded of the issue that toxo stores its >>> chromosome >>> sequence in VirtualSequence while the other two use >>> ExternalNaSequence. >>> >>> this means that we cannot re-use sql code, which is a headache. >>> >>> our proposed solution is to upgrade NaSequence view (the >>> superclass) to >>> have a source_id column. We feel that this is correct >>> semantically, >>> and also solves our problem. >>> >>> the semantics are that: >>> (1) NaSequence already has an external_database_release_id, which >>> makes no sense w/o source_id >>> (2) the pair (external_database_release_id, source_id) has >>> "universal" >>> semantics (ie, not just limited to "external" sequences). that >>> semantics is "dataset and stable_id" >>> >>> steve >>> _______________________________________________ >>> ApiDB mailing list >>> Ap...@pc... >>> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb >>> >>> >>> >> >> >> >> >> --------------------------------------------------------------------- >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Steve F. <sfi...@pc...> - 2007-03-02 21:19:38
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ok, great. no, source_id is string1 in one view and string2. we'd have to adjust that. in Api we plan on correcting this with a schema/data patch. steve pi...@pc... wrote: >I agree with this. In fact, the current database being used by our mammalian >DoTS build has incorporated a source_id into the assembly view of >NASequence. I >believe (could be wrong on this) that this is the only view without a >source_id. So this would clear the way to having source_id in the >super class >for the "official" GUS schema. Are all the nasequenceimp views using the same >field for source_id? Are there other views missing a source_id? > > > > >Quoting Steve Fischer <sfi...@pc...>: > > > >>folks- >> >>we've been again reminded of the issue that toxo stores its chromosome >>sequence in VirtualSequence while the other two use ExternalNaSequence. >> >>this means that we cannot re-use sql code, which is a headache. >> >>our proposed solution is to upgrade NaSequence view (the superclass) to >>have a source_id column. We feel that this is correct semantically, >>and also solves our problem. >> >>the semantics are that: >> (1) NaSequence already has an external_database_release_id, which >>makes no sense w/o source_id >> (2) the pair (external_database_release_id, source_id) has "universal" >>semantics (ie, not just limited to "external" sequences). that >>semantics is "dataset and stable_id" >> >>steve >>_______________________________________________ >>ApiDB mailing list >>Ap...@pc... >>https://mail.pcbi.upenn.edu/mailman/listinfo/apidb >> >> >> > > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: Chris S. <sto...@pc...> - 2007-03-02 20:48:35
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Debbie, Thanks for putting this out to the gusdev list. Has anyone added this to the GUS bug tracker for schema? Chris On Mar 2, 2007, at 3:46 PM, pi...@pc... wrote: > I agree with this. In fact, the current database being used by our > mammalian > DoTS build has incorporated a source_id into the assembly view of > NASequence. I > believe (could be wrong on this) that this is the only view without a > source_id. So this would clear the way to having source_id in the > super class > for the "official" GUS schema. Are all the nasequenceimp views > using the same > field for source_id? Are there other views missing a source_id? > > > > > Quoting Steve Fischer <sfi...@pc...>: > >> folks- >> >> we've been again reminded of the issue that toxo stores its >> chromosome >> sequence in VirtualSequence while the other two use >> ExternalNaSequence. >> >> this means that we cannot re-use sql code, which is a headache. >> >> our proposed solution is to upgrade NaSequence view (the >> superclass) to >> have a source_id column. We feel that this is correct semantically, >> and also solves our problem. >> >> the semantics are that: >> (1) NaSequence already has an external_database_release_id, which >> makes no sense w/o source_id >> (2) the pair (external_database_release_id, source_id) has >> "universal" >> semantics (ie, not just limited to "external" sequences). that >> semantics is "dataset and stable_id" >> >> steve >> _______________________________________________ >> ApiDB mailing list >> Ap...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb >> > > > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: <pi...@pc...> - 2007-03-02 20:46:16
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I agree with this. In fact, the current database being used by our mammalian DoTS build has incorporated a source_id into the assembly view of NASequence. I believe (could be wrong on this) that this is the only view without a source_id. So this would clear the way to having source_id in the super class for the "official" GUS schema. Are all the nasequenceimp views using the same field for source_id? Are there other views missing a source_id? Quoting Steve Fischer <sfi...@pc...>: > folks- > > we've been again reminded of the issue that toxo stores its chromosome > sequence in VirtualSequence while the other two use ExternalNaSequence. > > this means that we cannot re-use sql code, which is a headache. > > our proposed solution is to upgrade NaSequence view (the superclass) to > have a source_id column. We feel that this is correct semantically, > and also solves our problem. > > the semantics are that: > (1) NaSequence already has an external_database_release_id, which > makes no sense w/o source_id > (2) the pair (external_database_release_id, source_id) has "universal" > semantics (ie, not just limited to "external" sequences). that > semantics is "dataset and stable_id" > > steve > _______________________________________________ > ApiDB mailing list > Ap...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/apidb > |
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