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[GUSDEV] ISF error
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From: davila <da...@io...> - 2007-05-11 17:36:07
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Hi Folks, could anyone help to debug this error ?
ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir =
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank =
--extDbRlsVer 159.0
Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=3Dmydb
Fri May 11 13:20:31 2007 PLUGIN =
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 11 13:20:31 2007 ARG algoinvo 1
Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
Fri May 11 13:20:31 2007 ARG comment
Fri May 11 13:20:31 2007 ARG commit 0
Fri May 11 13:20:31 2007 ARG debug 0
Fri May 11 13:20:31 2007 ARG defaultOrganism
Fri May 11 13:20:31 2007 ARG extDbName GenBank
Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
Fri May 11 13:20:31 2007 ARG fileFormat genbank
Fri May 11 13:20:31 2007 ARG gff2GroupTag
Fri May 11 13:20:31 2007 ARG group
Fri May 11 13:20:31 2007 ARG gusconfigfile =
$GUS_HOME/config/gus.config
Fri May 11 13:20:31 2007 ARG handlerExternalDbs
Fri May 11 13:20:31 2007 ARG help
Fri May 11 13:20:31 2007 ARG helpHTML
Fri May 11 13:20:31 2007 ARG inputFileExtension
Fri May 11 13:20:31 2007 ARG inputFileOrDir =
/home/davila1/lguyanensis.gb
Fri May 11 13:20:31 2007 ARG mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
Fri May 11 13:20:31 2007 ARG naSequenceSubclass
Fri May 11 13:20:31 2007 ARG organism
Fri May 11 13:20:31 2007 ARG project
Fri May 11 13:20:31 2007 ARG seqExtDbName
Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
Fri May 11 13:20:31 2007 ARG seqSoTerm
Fri May 11 13:20:31 2007 ARG seqType
Fri May 11 13:20:31 2007 ARG soCvsVersion
Fri May 11 13:20:31 2007 ARG sqlVerbose 0
Fri May 11 13:20:31 2007 ARG testNumber
Fri May 11 13:20:31 2007 ARG user
Fri May 11 13:20:31 2007 ARG verbose 0
Fri May 11 13:20:31 2007 ARG veryVerbose 0
Fri May 11 13:20:31 2007 AlgInvocationId 61
Fri May 11 13:20:31 2007 COMMIT commit off
Fri May 11 13:20:31 2007 Processing file =
'/home/davila1/lguyanensis.gb'...
ERROR:
Attempting to get id from cache with null name at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
1103, <GEN32> line 65.
STACK TRACE:
at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm =
line 1103
=
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supp=
orted::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name', =
'taxon_id') called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
998
=
GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supporte=
d::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)') called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
645
=
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS:=
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
604
=
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
574
=
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Sup=
ported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
361
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd7f0)', 'HASH(0x20628f0)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
However, when I use --organism and --defaultOrganism the error changes:
ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir =
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank =
--extDbRlsVer 159.0 --organism "Leishmania guyanensis" --defaultOrganism =
"Leishmania guyanensis" --verbose
Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=3Dmydb
Fri May 11 13:21:54 2007 PLUGIN =
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 11 13:21:54 2007 ARG algoinvo 1
Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
Fri May 11 13:21:54 2007 ARG comment
Fri May 11 13:21:54 2007 ARG commit 0
Fri May 11 13:21:54 2007 ARG debug 0
Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania =
guyanensis
Fri May 11 13:21:54 2007 ARG extDbName GenBank
Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
Fri May 11 13:21:54 2007 ARG fileFormat genbank
Fri May 11 13:21:54 2007 ARG gff2GroupTag
Fri May 11 13:21:54 2007 ARG group
Fri May 11 13:21:54 2007 ARG gusconfigfile =
$GUS_HOME/config/gus.config
Fri May 11 13:21:54 2007 ARG handlerExternalDbs
Fri May 11 13:21:54 2007 ARG help
Fri May 11 13:21:54 2007 ARG helpHTML
Fri May 11 13:21:54 2007 ARG inputFileExtension
Fri May 11 13:21:54 2007 ARG inputFileOrDir =
/home/davila1/lguyanensis.gb
Fri May 11 13:21:54 2007 ARG mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
Fri May 11 13:21:54 2007 ARG naSequenceSubclass
Fri May 11 13:21:54 2007 ARG organism Leishmania =
guyanensis
Fri May 11 13:21:54 2007 ARG project
Fri May 11 13:21:54 2007 ARG seqExtDbName
Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
Fri May 11 13:21:54 2007 ARG seqSoTerm
Fri May 11 13:21:54 2007 ARG seqType
Fri May 11 13:21:54 2007 ARG soCvsVersion
Fri May 11 13:21:54 2007 ARG sqlVerbose 0
Fri May 11 13:21:54 2007 ARG testNumber
Fri May 11 13:21:54 2007 ARG user
Fri May 11 13:21:54 2007 ARG verbose 1
Fri May 11 13:21:54 2007 ARG veryVerbose 0
Fri May 11 13:21:54 2007 AlgInvocationId 62
Fri May 11 13:21:54 2007 COMMIT commit off
Fri May 11 13:21:54 2007 Processing file =
'/home/davila1/lguyanensis.gb'...
ERROR:
Can't run bioperlSeq preprocessor method =
'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
=20
ERROR:
Undefined subroutine =
&GUS::Supported::UnflattenBioperlFeatures::preprocess called at =
$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63, =
<GEN32> line 65.
STACK TRACE:
at /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm =
line 63
eval {...} called at =
$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
=
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)', 'HASH(0x2062960)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
STACK TRACE:
at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
=
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)', 'HASH(0x2062960)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy =
(*.dmp) file from May 11 2007, apparently it does not make a new load, =
but updates the respective Sres tables, anyway such as the first run the =
re-run of LoadTaxon provided these warnings:
Fri May 11 12:42:27 2007 Merging taxons
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not in =
database, skipping
What this exactly means ?
The first time I ran LoadTaxon I got this log:
tail LoadTaxon.log=20
Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
Mon May 7 00:07:39 2007 0 TaxonName entries deleted
Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
Mon May 7 00:07:42 2007 RESULT 1
Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
Mon May 7 00:07:47 2007 AlgInvocationId 7
Mon May 7 00:07:47 2007 COMMIT commit on
The second time:
tail LoadTaxon_new.log=20
Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
Fri May 11 13:07:51 2007 288 TaxonName entries deleted
Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
Fri May 11 13:07:55 2007 RESULT 1
Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
Fri May 11 13:07:56 2007 AlgInvocationId 56
Fri May 11 13:07:56 2007 COMMIT commit on
I just checked the sres.taxonname and it has Leishmania guyanensis =
there:
SELECT =
"taxon_name_id","taxon_id","name","unique_name_variant","name_class","mod=
ification_date","row_project_id","row_alg_invocation_id" FROM =
"sres"."taxonname" WHERE=20
"name" =3D 'Leishmania guyanensis';
taxon_name_id | taxon_id | name | unique_name_variant =
| name_class | modification_date | row_project_id | =
row_alg_invocation_id=20
---------------+----------+-----------------------+---------------------+=
-----------------+---------------------------+----------------+----------=
-------------
369208 | 96595 | Leishmania guyanensis | =
| scientific name | 2007-05-06 23:41:16.98889 | 1 | =
7
(1 row)
According to the log, it could be an =
UnflattenBioperlFeatures::preprocess error too...
Some of th GIs (L. guyanensis) I am trying to load with the ISF pluging =
are:
104530485
60280340
110816091
76577720
76577719
76577718
Thanks for any help you might provide.
Cheers, Alberto
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