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Re: [GUSDEV] RES: ISF error
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From: Steve F. <sfi...@pc...> - 2007-05-18 16:16:34
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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
>> >
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
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>>
>> ------------------------------------------------------------------------
>>
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>
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