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Re: [GUSDEV] RES: ISF error
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From: Alberto D. <da...@io...> - 2007-05-18 15:48:04
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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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--
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
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