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From: davila <da...@io...> - 2007-05-11 17:36:07
|
Hi Folks, could anyone help to debug this error ?
ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir =
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank =
--extDbRlsVer 159.0
Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=3Dmydb
Fri May 11 13:20:31 2007 PLUGIN =
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 11 13:20:31 2007 ARG algoinvo 1
Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
Fri May 11 13:20:31 2007 ARG comment
Fri May 11 13:20:31 2007 ARG commit 0
Fri May 11 13:20:31 2007 ARG debug 0
Fri May 11 13:20:31 2007 ARG defaultOrganism
Fri May 11 13:20:31 2007 ARG extDbName GenBank
Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
Fri May 11 13:20:31 2007 ARG fileFormat genbank
Fri May 11 13:20:31 2007 ARG gff2GroupTag
Fri May 11 13:20:31 2007 ARG group
Fri May 11 13:20:31 2007 ARG gusconfigfile =
$GUS_HOME/config/gus.config
Fri May 11 13:20:31 2007 ARG handlerExternalDbs
Fri May 11 13:20:31 2007 ARG help
Fri May 11 13:20:31 2007 ARG helpHTML
Fri May 11 13:20:31 2007 ARG inputFileExtension
Fri May 11 13:20:31 2007 ARG inputFileOrDir =
/home/davila1/lguyanensis.gb
Fri May 11 13:20:31 2007 ARG mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
Fri May 11 13:20:31 2007 ARG naSequenceSubclass
Fri May 11 13:20:31 2007 ARG organism
Fri May 11 13:20:31 2007 ARG project
Fri May 11 13:20:31 2007 ARG seqExtDbName
Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
Fri May 11 13:20:31 2007 ARG seqSoTerm
Fri May 11 13:20:31 2007 ARG seqType
Fri May 11 13:20:31 2007 ARG soCvsVersion
Fri May 11 13:20:31 2007 ARG sqlVerbose 0
Fri May 11 13:20:31 2007 ARG testNumber
Fri May 11 13:20:31 2007 ARG user
Fri May 11 13:20:31 2007 ARG verbose 0
Fri May 11 13:20:31 2007 ARG veryVerbose 0
Fri May 11 13:20:31 2007 AlgInvocationId 61
Fri May 11 13:20:31 2007 COMMIT commit off
Fri May 11 13:20:31 2007 Processing file =
'/home/davila1/lguyanensis.gb'...
ERROR:
Attempting to get id from cache with null name at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
1103, <GEN32> line 65.
STACK TRACE:
at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm =
line 1103
=
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supp=
orted::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name', =
'taxon_id') called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
998
=
GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supporte=
d::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)') called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
645
=
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS:=
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
604
=
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
574
=
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Sup=
ported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
361
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd7f0)', 'HASH(0x20628f0)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
However, when I use --organism and --defaultOrganism the error changes:
ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir =
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank =
--extDbRlsVer 159.0 --organism "Leishmania guyanensis" --defaultOrganism =
"Leishmania guyanensis" --verbose
Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=3Dmydb
Fri May 11 13:21:54 2007 PLUGIN =
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 11 13:21:54 2007 ARG algoinvo 1
Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
Fri May 11 13:21:54 2007 ARG comment
Fri May 11 13:21:54 2007 ARG commit 0
Fri May 11 13:21:54 2007 ARG debug 0
Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania =
guyanensis
Fri May 11 13:21:54 2007 ARG extDbName GenBank
Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
Fri May 11 13:21:54 2007 ARG fileFormat genbank
Fri May 11 13:21:54 2007 ARG gff2GroupTag
Fri May 11 13:21:54 2007 ARG group
Fri May 11 13:21:54 2007 ARG gusconfigfile =
$GUS_HOME/config/gus.config
Fri May 11 13:21:54 2007 ARG handlerExternalDbs
Fri May 11 13:21:54 2007 ARG help
Fri May 11 13:21:54 2007 ARG helpHTML
Fri May 11 13:21:54 2007 ARG inputFileExtension
Fri May 11 13:21:54 2007 ARG inputFileOrDir =
/home/davila1/lguyanensis.gb
Fri May 11 13:21:54 2007 ARG mapFile =
$PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
Fri May 11 13:21:54 2007 ARG naSequenceSubclass
Fri May 11 13:21:54 2007 ARG organism Leishmania =
guyanensis
Fri May 11 13:21:54 2007 ARG project
Fri May 11 13:21:54 2007 ARG seqExtDbName
Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
Fri May 11 13:21:54 2007 ARG seqSoTerm
Fri May 11 13:21:54 2007 ARG seqType
Fri May 11 13:21:54 2007 ARG soCvsVersion
Fri May 11 13:21:54 2007 ARG sqlVerbose 0
Fri May 11 13:21:54 2007 ARG testNumber
Fri May 11 13:21:54 2007 ARG user
Fri May 11 13:21:54 2007 ARG verbose 1
Fri May 11 13:21:54 2007 ARG veryVerbose 0
Fri May 11 13:21:54 2007 AlgInvocationId 62
Fri May 11 13:21:54 2007 COMMIT commit off
Fri May 11 13:21:54 2007 Processing file =
'/home/davila1/lguyanensis.gb'...
ERROR:
Can't run bioperlSeq preprocessor method =
'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
=20
ERROR:
Undefined subroutine =
&GUS::Supported::UnflattenBioperlFeatures::preprocess called at =
$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63, =
<GEN32> line 65.
STACK TRACE:
at /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm =
line 63
eval {...} called at =
$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
=
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)', 'HASH(0x2062960)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
STACK TRACE:
at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
=
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)', =
'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)') =
called at =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
=
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)', 'HASH(0x2062960)') called =
at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
=
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
=
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)', =
'GUS::Supported::Plugin::InsertSequenceFeatures') called at =
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
=
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'GUS::Supported::Plugin::InsertSequenceFeatures') =
called at $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
=
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)', 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line =
11
Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy =
(*.dmp) file from May 11 2007, apparently it does not make a new load, =
but updates the respective Sres tables, anyway such as the first run the =
re-run of LoadTaxon provided these warnings:
Fri May 11 12:42:27 2007 Merging taxons
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not in =
database, skipping
Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not in =
database, skipping
What this exactly means ?
The first time I ran LoadTaxon I got this log:
tail LoadTaxon.log=20
Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
Mon May 7 00:07:39 2007 0 TaxonName entries deleted
Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
Mon May 7 00:07:42 2007 RESULT 1
Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
Mon May 7 00:07:47 2007 AlgInvocationId 7
Mon May 7 00:07:47 2007 COMMIT commit on
The second time:
tail LoadTaxon_new.log=20
Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
Fri May 11 13:07:51 2007 288 TaxonName entries deleted
Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
Fri May 11 13:07:55 2007 RESULT 1
Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
Fri May 11 13:07:56 2007 AlgInvocationId 56
Fri May 11 13:07:56 2007 COMMIT commit on
I just checked the sres.taxonname and it has Leishmania guyanensis =
there:
SELECT =
"taxon_name_id","taxon_id","name","unique_name_variant","name_class","mod=
ification_date","row_project_id","row_alg_invocation_id" FROM =
"sres"."taxonname" WHERE=20
"name" =3D 'Leishmania guyanensis';
taxon_name_id | taxon_id | name | unique_name_variant =
| name_class | modification_date | row_project_id | =
row_alg_invocation_id=20
---------------+----------+-----------------------+---------------------+=
-----------------+---------------------------+----------------+----------=
-------------
369208 | 96595 | Leishmania guyanensis | =
| scientific name | 2007-05-06 23:41:16.98889 | 1 | =
7
(1 row)
According to the log, it could be an =
UnflattenBioperlFeatures::preprocess error too...
Some of th GIs (L. guyanensis) I am trying to load with the ISF pluging =
are:
104530485
60280340
110816091
76577720
76577719
76577718
Thanks for any help you might provide.
Cheers, Alberto
|
|
From: Steve F. <sfi...@pc...> - 2007-05-11 18:02:05
|
it looks as though it is trying to find the taxon of the sequence but is
coming up with a null (see the method getTaxonId in the plugin).
if the file contains all one species, you can provide that on the
command line.
otherwise, you'll need to look at the plugin code to see where in the
files it is expecting to find that info and correct the files so that it
is there.
steve
davila wrote:
>
> Hi Folks, could anyone help to debug this error ?
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=mydb
> Fri May 11 13:20:31 2007 PLUGIN
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:20:31 2007 ARG algoinvo 1
> Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:20:31 2007 ARG comment
> Fri May 11 13:20:31 2007 ARG commit 0
> Fri May 11 13:20:31 2007 ARG debug 0
> Fri May 11 13:20:31 2007 ARG defaultOrganism
> Fri May 11 13:20:31 2007 ARG extDbName GenBank
> Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 ARG fileFormat genbank
> Fri May 11 13:20:31 2007 ARG gff2GroupTag
> Fri May 11 13:20:31 2007 ARG group
> Fri May 11 13:20:31 2007 ARG gusconfigfile
> $GUS_HOME/config/gus.config
> Fri May 11 13:20:31 2007 ARG handlerExternalDbs
> Fri May 11 13:20:31 2007 ARG help
> Fri May 11 13:20:31 2007 ARG helpHTML
> Fri May 11 13:20:31 2007 ARG inputFileExtension
> Fri May 11 13:20:31 2007 ARG inputFileOrDir
> /home/davila1/lguyanensis.gb
> Fri May 11 13:20:31 2007 ARG mapFile
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:20:31 2007 ARG naSequenceSubclass
> Fri May 11 13:20:31 2007 ARG organism
> Fri May 11 13:20:31 2007 ARG project
> Fri May 11 13:20:31 2007 ARG seqExtDbName
> Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
> Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
> Fri May 11 13:20:31 2007 ARG seqSoTerm
> Fri May 11 13:20:31 2007 ARG seqType
> Fri May 11 13:20:31 2007 ARG soCvsVersion
> Fri May 11 13:20:31 2007 ARG sqlVerbose 0
> Fri May 11 13:20:31 2007 ARG testNumber
> Fri May 11 13:20:31 2007 ARG user
> Fri May 11 13:20:31 2007 ARG verbose 0
> Fri May 11 13:20:31 2007 ARG veryVerbose 0
> Fri May 11 13:20:31 2007 AlgInvocationId 61
> Fri May 11 13:20:31 2007 COMMIT commit off
> Fri May 11 13:20:31 2007 Processing file
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Attempting to get id from cache with null name at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 1103, <GEN32> line 65.
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 1103
>
> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
> 'taxon_id') called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 998
>
> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 645
>
> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 604
>
> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 574
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 361
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> 'HASH(0x20628f0)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
> However, when I use --organism and --defaultOrganism the error changes:
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
> --defaultOrganism "Leishmania guyanensis" --verbose
> Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=mydb
> Fri May 11 13:21:54 2007 PLUGIN
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:21:54 2007 ARG algoinvo 1
> Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:21:54 2007 ARG comment
> Fri May 11 13:21:54 2007 ARG commit 0
> Fri May 11 13:21:54 2007 ARG debug 0
> Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania
> guyanensis
> Fri May 11 13:21:54 2007 ARG extDbName GenBank
> Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:21:54 2007 ARG fileFormat genbank
> Fri May 11 13:21:54 2007 ARG gff2GroupTag
> Fri May 11 13:21:54 2007 ARG group
> Fri May 11 13:21:54 2007 ARG gusconfigfile
> $GUS_HOME/config/gus.config
> Fri May 11 13:21:54 2007 ARG handlerExternalDbs
> Fri May 11 13:21:54 2007 ARG help
> Fri May 11 13:21:54 2007 ARG helpHTML
> Fri May 11 13:21:54 2007 ARG inputFileExtension
> Fri May 11 13:21:54 2007 ARG inputFileOrDir
> /home/davila1/lguyanensis.gb
> Fri May 11 13:21:54 2007 ARG mapFile
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:21:54 2007 ARG naSequenceSubclass
> Fri May 11 13:21:54 2007 ARG organism Leishmania
> guyanensis
> Fri May 11 13:21:54 2007 ARG project
> Fri May 11 13:21:54 2007 ARG seqExtDbName
> Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
> Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
> Fri May 11 13:21:54 2007 ARG seqSoTerm
> Fri May 11 13:21:54 2007 ARG seqType
> Fri May 11 13:21:54 2007 ARG soCvsVersion
> Fri May 11 13:21:54 2007 ARG sqlVerbose 0
> Fri May 11 13:21:54 2007 ARG testNumber
> Fri May 11 13:21:54 2007 ARG user
> Fri May 11 13:21:54 2007 ARG verbose 1
> Fri May 11 13:21:54 2007 ARG veryVerbose 0
> Fri May 11 13:21:54 2007 AlgInvocationId 62
> Fri May 11 13:21:54 2007 COMMIT commit off
> Fri May 11 13:21:54 2007 Processing file
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Can't run bioperlSeq preprocessor method
> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
>
> ERROR:
> Undefined subroutine
> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
> <GEN32> line 65.
>
> STACK TRACE:
> at
> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
> line 63
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
>
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 365
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> 'HASH(0x2062960)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
>
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> called at
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 365
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> 'HASH(0x2062960)') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
> Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy
> (*.dmp) file from May 11 2007, apparently it does not make a new load,
> but updates the respective Sres tables, anyway such as the first run
> the re-run of LoadTaxon provided these warnings:
>
> Fri May 11 12:42:27 2007 Merging taxons
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not
> in database, skipping
>
> What this exactly means ?
>
> The first time I ran LoadTaxon I got this log:
>
> tail LoadTaxon.log
> Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
> Mon May 7 00:07:39 2007 0 TaxonName entries deleted
>
> Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
> Mon May 7 00:07:42 2007 RESULT 1
> Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
> Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
> Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
> Mon May 7 00:07:47 2007 AlgInvocationId 7
> Mon May 7 00:07:47 2007 COMMIT commit on
>
> The second time:
>
> tail LoadTaxon_new.log
> Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
> Fri May 11 13:07:51 2007 288 TaxonName entries deleted
>
> Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
> Fri May 11 13:07:55 2007 RESULT 1
> Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
> Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
> Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
> Fri May 11 13:07:56 2007 AlgInvocationId 56
> Fri May 11 13:07:56 2007 COMMIT commit on
>
> I just checked the sres.taxonname and it has Leishmania guyanensis there:
>
> SELECT
> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
> FROM "sres"."taxonname" WHERE
> "name" = 'Leishmania guyanensis';
> taxon_name_id | taxon_id | name |
> unique_name_variant | name_class | modification_date |
> row_project_id | row_alg_invocation_id
> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
> 369208 | 96595 | Leishmania guyanensis
> | | scientific name | 2007-05-06 23:41:16.98889
> | 1 | 7
> (1 row)
>
> According to the log, it could be an
> UnflattenBioperlFeatures::preprocess error too...
>
> Some of th GIs (L. guyanensis) I am trying to load with the ISF
> pluging are:
>
> 104530485
> 60280340
> 110816091
> 76577720
> 76577719
> 76577718
>
> Thanks for any help you might provide.
>
> Cheers, Alberto
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
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> ------------------------------------------------------------------------
>
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: davila <da...@io...> - 2007-05-12 16:39:48
|
Thanks Steve !
I will open the script and check it, however, is this a GUS plugin : =
"GUS::Supported::UnflattenBioperlFeatures::preprocess" ? if so, it is =
not available at $GUS_HOME or $PROJECT_HOME plugin directories:
[davila1@kineto4 Supported]$ ls -lh =
$PROJECT_HOME/GUS/Supported/plugin/perl/
total 668K
-rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
-rw-r--r-- 1 davila1 gus 12K May 3 17:12 =
CalculateTranslatedAASequences.pm
-rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
-rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
-rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
-rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
-rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
-rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
-rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 =
InsertOntologyRelationshipType.pm
-rw-r--r-- 1 davila1 gus 16K May 3 17:12 =
InsertOntologyTermsAndRelationships.pm
-rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
-rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
-rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
-rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
-rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
-rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
-rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
-rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
-rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
-rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
-rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
drwxr-xr-x 3 davila1 gus 4.0K May 3 17:12 Test
[davila1@kineto4 Supported]$ ls -lh =
$GUS_HOME/lib/perl/GUS/Supported/Plugin/
total 668K
-rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
-rw-r--r-- 1 davila1 gus 12K May 3 17:12 =
CalculateTranslatedAASequences.pm
-rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
-rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
-rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
-rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
-rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
-rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
-rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
-rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
-rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 =
InsertOntologyRelationshipType.pm
-rw-r--r-- 1 davila1 gus 16K May 3 17:12 =
InsertOntologyTermsAndRelationships.pm
-rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
-rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
-rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
-rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
-rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
-rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
-rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
-rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
-rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
-rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
-rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
-rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
-rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
-rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
-rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
-rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
drwxr-xr-x 2 davila1 gus 4.0K May 3 17:12 Test
This is the part of the =
"$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm" plugin =
originating the error:
sub preprocessBioperlSeq {
my ($self, $bioperlSeq) =3D @_;
return unless $self->{bioperlSeqPreprocessor};
my $class =3D $self->{bioperlSeqPreprocessor}->{class};
eval {
no strict "refs";
eval "require $class";
my $method =3D "${class}::preprocess";
&$method($bioperlSeq); ### Line 63 originating the error #####
};
my $err =3D $@;
if ($err) { die "Can't run bioperlSeq preprocessor method =
'${class}::preprocess'. Error:\n $err\n"; }
}
Where I can find "$bioperlSeq" ?
Thanks, Alberto
-----Mensagem original-----
De: Steve Fischer [mailto:sfi...@pc...]
Enviada: sex 11-mai-07 3:01
Para: davila
Cc: gus...@li...; mro...@cs...; =
cj...@fr...
Assunto: Re: [GUSDEV] ISF error
=20
it looks as though it is trying to find the taxon of the sequence but is =
coming up with a null (see the method getTaxonId in the plugin).
if the file contains all one species, you can provide that on the=20
command line.
otherwise, you'll need to look at the plugin code to see where in the=20
files it is expecting to find that info and correct the files so that it =
is there.
steve
davila wrote:
>
> Hi Folks, could anyone help to debug this error ?
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir=20
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank=20
> --extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=3Dmydb
> Fri May 11 13:20:31 2007 PLUGIN =20
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:20:31 2007 ARG algoinvo 1
> Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:20:31 2007 ARG comment
> Fri May 11 13:20:31 2007 ARG commit 0
> Fri May 11 13:20:31 2007 ARG debug 0
> Fri May 11 13:20:31 2007 ARG defaultOrganism
> Fri May 11 13:20:31 2007 ARG extDbName GenBank
> Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:20:31 2007 ARG fileFormat genbank
> Fri May 11 13:20:31 2007 ARG gff2GroupTag
> Fri May 11 13:20:31 2007 ARG group
> Fri May 11 13:20:31 2007 ARG gusconfigfile =20
> $GUS_HOME/config/gus.config
> Fri May 11 13:20:31 2007 ARG handlerExternalDbs
> Fri May 11 13:20:31 2007 ARG help
> Fri May 11 13:20:31 2007 ARG helpHTML
> Fri May 11 13:20:31 2007 ARG inputFileExtension
> Fri May 11 13:20:31 2007 ARG inputFileOrDir =20
> /home/davila1/lguyanensis.gb
> Fri May 11 13:20:31 2007 ARG mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:20:31 2007 ARG naSequenceSubclass
> Fri May 11 13:20:31 2007 ARG organism
> Fri May 11 13:20:31 2007 ARG project
> Fri May 11 13:20:31 2007 ARG seqExtDbName
> Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
> Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
> Fri May 11 13:20:31 2007 ARG seqSoTerm
> Fri May 11 13:20:31 2007 ARG seqType
> Fri May 11 13:20:31 2007 ARG soCvsVersion
> Fri May 11 13:20:31 2007 ARG sqlVerbose 0
> Fri May 11 13:20:31 2007 ARG testNumber
> Fri May 11 13:20:31 2007 ARG user
> Fri May 11 13:20:31 2007 ARG verbose 0
> Fri May 11 13:20:31 2007 ARG veryVerbose 0
> Fri May 11 13:20:31 2007 AlgInvocationId 61
> Fri May 11 13:20:31 2007 COMMIT commit off
> Fri May 11 13:20:31 2007 Processing file=20
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Attempting to get id from cache with null name at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
> 1103, <GEN32> line 65.
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm=20
> line 1103
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supp=
orted::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',=20
> 'taxon_id') called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
998
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supporte=
d::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)') called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
645
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS:=
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
604
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
574
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Sup=
ported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe130)', 171) called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
361
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd7f0)',=20
> 'HASH(0x20628f0)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
> However, when I use --organism and --defaultOrganism the error =
changes:
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir=20
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank=20
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"=20
> --defaultOrganism "Leishmania guyanensis" --verbose
> Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=3Dmydb
> Fri May 11 13:21:54 2007 PLUGIN =20
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 11 13:21:54 2007 ARG algoinvo 1
> Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
> Fri May 11 13:21:54 2007 ARG comment
> Fri May 11 13:21:54 2007 ARG commit 0
> Fri May 11 13:21:54 2007 ARG debug 0
> Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania=20
> guyanensis
> Fri May 11 13:21:54 2007 ARG extDbName GenBank
> Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
> Fri May 11 13:21:54 2007 ARG fileFormat genbank
> Fri May 11 13:21:54 2007 ARG gff2GroupTag
> Fri May 11 13:21:54 2007 ARG group
> Fri May 11 13:21:54 2007 ARG gusconfigfile =20
> $GUS_HOME/config/gus.config
> Fri May 11 13:21:54 2007 ARG handlerExternalDbs
> Fri May 11 13:21:54 2007 ARG help
> Fri May 11 13:21:54 2007 ARG helpHTML
> Fri May 11 13:21:54 2007 ARG inputFileExtension
> Fri May 11 13:21:54 2007 ARG inputFileOrDir =20
> /home/davila1/lguyanensis.gb
> Fri May 11 13:21:54 2007 ARG mapFile=20
> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> Fri May 11 13:21:54 2007 ARG naSequenceSubclass
> Fri May 11 13:21:54 2007 ARG organism Leishmania=20
> guyanensis
> Fri May 11 13:21:54 2007 ARG project
> Fri May 11 13:21:54 2007 ARG seqExtDbName
> Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
> Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
> Fri May 11 13:21:54 2007 ARG seqSoTerm
> Fri May 11 13:21:54 2007 ARG seqType
> Fri May 11 13:21:54 2007 ARG soCvsVersion
> Fri May 11 13:21:54 2007 ARG sqlVerbose 0
> Fri May 11 13:21:54 2007 ARG testNumber
> Fri May 11 13:21:54 2007 ARG user
> Fri May 11 13:21:54 2007 ARG verbose 1
> Fri May 11 13:21:54 2007 ARG veryVerbose 0
> Fri May 11 13:21:54 2007 AlgInvocationId 62
> Fri May 11 13:21:54 2007 COMMIT commit off
> Fri May 11 13:21:54 2007 Processing file=20
> '/home/davila1/lguyanensis.gb'...
>
> ERROR:
> Can't run bioperlSeq preprocessor method=20
> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
>
> ERROR:
> Undefined subroutine=20
> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at=20
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,=20
> <GEN32> line 65.
>
> STACK TRACE:
> at=20
> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm=20
> line 63
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
> =20
> =
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)')=20
> called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)',=20
> 'HASH(0x2062960)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
>
>
> STACK TRACE:
> at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
> =20
> =
GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supporte=
d::BioperlFeatMapperSet=3DHASH(0x207c9c0)',=20
> 'Bio::Seq::RichSeq=3DHASH(0x28fe2d0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0xfdd9b0)')=20
> called at=20
> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line =
365
> =20
> =
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0xfdd9b0)',=20
> 'HASH(0x2062960)') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> =20
> =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> =20
> =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x5052a0)',=20
> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>
> Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy =
> (*.dmp) file from May 11 2007, apparently it does not make a new load, =
> but updates the respective Sres tables, anyway such as the first run=20
> the re-run of LoadTaxon provided these warnings:
>
> Fri May 11 12:42:27 2007 Merging taxons
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not=20
> in database, skipping
> Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not=20
> in database, skipping
>
> What this exactly means ?
>
> The first time I ran LoadTaxon I got this log:
>
> tail LoadTaxon.log
> Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
> Mon May 7 00:07:39 2007 0 TaxonName entries deleted
>
> Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
> Mon May 7 00:07:42 2007 RESULT 1
> Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
> Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
> Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
> Mon May 7 00:07:47 2007 AlgInvocationId 7
> Mon May 7 00:07:47 2007 COMMIT commit on
>
> The second time:
>
> tail LoadTaxon_new.log
> Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
> Fri May 11 13:07:51 2007 288 TaxonName entries deleted
>
> Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
> Fri May 11 13:07:55 2007 RESULT 1
> Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
> Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
> Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
> Fri May 11 13:07:56 2007 AlgInvocationId 56
> Fri May 11 13:07:56 2007 COMMIT commit on
>
> I just checked the sres.taxonname and it has Leishmania guyanensis =
there:
>
> SELECT=20
> =
"taxon_name_id","taxon_id","name","unique_name_variant","name_class","mod=
ification_date","row_project_id","row_alg_invocation_id"=20
> FROM "sres"."taxonname" WHERE
> "name" =3D 'Leishmania guyanensis';
> taxon_name_id | taxon_id | name |=20
> unique_name_variant | name_class | modification_date |=20
> row_project_id | row_alg_invocation_id
> =
---------------+----------+-----------------------+---------------------+=
-----------------+---------------------------+----------------+----------=
-------------
> 369208 | 96595 | Leishmania guyanensis=20
> | | scientific name | 2007-05-06 23:41:16.98889=20
> | 1 | 7
> (1 row)
>
> According to the log, it could be an=20
> UnflattenBioperlFeatures::preprocess error too...
>
> Some of th GIs (L. guyanensis) I am trying to load with the ISF=20
> pluging are:
>
> 104530485
> 60280340
> 110816091
> 76577720
> 76577719
> 76577718
>
> Thanks for any help you might provide.
>
> Cheers, Alberto
>
|
|
From: Alberto D. <da...@io...> - 2007-05-18 15:48:04
|
Hi folks !
We managed to pass several errors with ISF but this one is a bit strange:
[davila1@kineto4 log]$ ga GUS::Supported::Plugin::InsertSequenceFeatures
--mapFile /system/GUS/gus_home/config/genbank2gus.xml --inputFileOrDir
/home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
--extDbRlsVer 159.0 --organism "Leishmania guyanensis" --defaultOrganism
"Leishmania guyanensis" --verbose --soCvsVersion 1.45
Fri May 18 12:42:57 2007 DSN dbi:Pg:dbname=protozoa
Fri May 18 12:42:57 2007 PLUGIN
GUS::Supported::Plugin::InsertSequenceFeatures
Fri May 18 12:42:57 2007 ARG algoinvo 1
Fri May 18 12:42:57 2007 ARG bioperlTreeOutput 0
Fri May 18 12:42:57 2007 ARG comment
Fri May 18 12:42:57 2007 ARG commit 0
Fri May 18 12:42:57 2007 ARG debug 0
Fri May 18 12:42:57 2007 ARG defaultOrganism Leishmania
guyanensis
Fri May 18 12:42:57 2007 ARG extDbName GenBank
Fri May 18 12:42:57 2007 ARG extDbRlsVer 159.0
Fri May 18 12:42:57 2007 ARG fileFormat genbank
Fri May 18 12:42:57 2007 ARG gff2GroupTag
Fri May 18 12:42:57 2007 ARG group
Fri May 18 12:42:57 2007 ARG gusconfigfile
/system/GUS/gus_home/config/gus.config
Fri May 18 12:42:57 2007 ARG handlerExternalDbs
Fri May 18 12:42:57 2007 ARG help
Fri May 18 12:42:57 2007 ARG helpHTML
Fri May 18 12:42:57 2007 ARG inputFileExtension
Fri May 18 12:42:57 2007 ARG inputFileOrDir
/home/davila1/lguyanensis.gb
Fri May 18 12:42:57 2007 ARG mapFile
/system/GUS/gus_home/config/genbank2gus.xml
Fri May 18 12:42:57 2007 ARG naSequenceSubclass
Fri May 18 12:42:57 2007 ARG organism Leishmania
guyanensis
Fri May 18 12:42:57 2007 ARG project
Fri May 18 12:42:57 2007 ARG seqExtDbName
Fri May 18 12:42:57 2007 ARG seqExtDbRlsVer
Fri May 18 12:42:57 2007 ARG seqIdColumn source_id
Fri May 18 12:42:57 2007 ARG seqSoTerm
Fri May 18 12:42:57 2007 ARG seqType
Fri May 18 12:42:57 2007 ARG soCvsVersion 1.45
Fri May 18 12:42:57 2007 ARG sqlVerbose 0
Fri May 18 12:42:57 2007 ARG testNumber
Fri May 18 12:42:57 2007 ARG user
Fri May 18 12:42:57 2007 ARG verbose 1
Fri May 18 12:42:57 2007 ARG veryVerbose 0
Fri May 18 12:42:57 2007 AlgInvocationId 83
Fri May 18 12:42:57 2007 COMMIT commit off
Fri May 18 12:42:58 2007 Processing file
'/home/davila1/lguyanensis.gb'...
DBD::Pg::st execute failed: ERROR: duplicate key violates unique
constraint "pk_externaldatabase"
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.ExternalDatabase ( group_write, other_read,
group_read, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
Values: 1, 1, 1, HSSP, 1, 1, 18, 0, 83, 1, 1, 1 at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
'\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
'HASH(0x30d4870)') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 160
GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 134
GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 117
GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 106
GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 1021
GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 891
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 771
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 367
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HASH(0x2062a70)') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
STACK TRACE:
at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
'\x{a} INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
'HASH(0x30d4870)') called at
/system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 160
GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 134
GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 117
GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HSSP:P07711') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
line 106
GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 1021
GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 891
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 897
GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 771
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
/system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 367
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
'HASH(0x2062a70)') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
eval {...} called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
This is my external_database table:
-- PostgreSQL database dump
--
SET client_encoding = 'UTF8';
SET standard_conforming_strings = off;
SET check_function_bodies = false;
SET client_min_messages = warning;
SET escape_string_warning = off;
SET search_path = sres, pg_catalog;
COPY externaldatabase (external_database_id, name, modification_date,
user_read, user_write, group_read, group_write, other_read, other_write,
row_user_id, row_group_id, row_project_id, row_alg_invocation_id) FROM
stdin;
164 RepBase 4.03 zebrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
106 maize-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2093 homstrad 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
89 mim 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1 assembly 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
154 RepBase 4.03 celrep.ref 4.0.4 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
82 mendel 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
185 RIKEN/FANTOM 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
292 Plasmodium_GSS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
102 hsc-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2096 PRODOM 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
189 COMPEL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3010 GeneDB_Lmajor 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2095 load 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
97 subtilist 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
90 mgd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
17 GSDB 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
92 aarhus/ghent-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
8 Brookhaven Protein Data Bank (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
184 ORNL GRAILExp gene predictions 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
12 GenPept 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
692 Plasmodium_TIGR 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
144 flybase translated orfs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3008 GeneDB_Afumigatus 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
165 RepBase 4.03 humsub.ref 1.0.2 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
13 IMAGE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
94 ecogene 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3024 GOA 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3011 GeneDB_Pberghei 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3018 GeneDB_Bpertussis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1392 CDD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3 EMBL Data Library (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2097 PFAMA 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
172 URL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
108 hiv 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
101 stygene 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3014 GeneDB_Tannulata 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
181 Signaling PAthway Database (SPAD) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
10 GenInfo Backbone Id (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2092 dbSNP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
78 embl 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
84 prosite 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3025 PubMed 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
6 Protein Research Foundation (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
928 GI 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
85 flybase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
14 EGAD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
126 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1792 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
156 RepBase 4.03 humrep.ref 7.0.6 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
152 TUBERCULIST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3005 GOC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
392 EPCon 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1892 PID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
98 eco2dbase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
104 transfac 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
293 Plasmodium_EST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
127 sptrembl 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
130 imgt/ligm 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1292 RATMAP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1192 ATCC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3001 GO Function 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
124 SWISS-PROT 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1494 CDD-Pfam 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
143 NCBI genomic Homo Sapiens 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
18 DOTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
133 estlib 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
161 RepBase 4.03 rodrep.ref 3.3.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
157 RepBase 4.03 invrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1495 CDD-Smart 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
79 pfam 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
103 carbbank 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
191 Whitehead Institute/MIT Center for Genome Research Mouse RH Map
2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
155 RepBase 4.03 drorep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
125 PSEUDO 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3006 GeneDB_Spombe 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3022 PMID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
153 RepBase 4.03 athrep.ref 4.0.5 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
122 SPTREMBL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
186 UCSC human draft genomic sequence (October 7 release) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
179 GeneMap 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
135 agis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3013 GeneDB_Pfalciparum 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
170 Pfam expert 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
178 StemCellDB public 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
149 Bucan lab. mouse BAC ends 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
148 Prodom 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3012 GeneDB_Pchabaudi 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
128 pseudo 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
175 INTERPRO 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
80 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3002 GO Component 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
21 gss_human_bak.seq 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1293 RGD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
9 Patents (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
15 BLOCKS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
37 swissprot 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2 GenBank (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
20 dbEST 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
166 Demeter 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
5 NBRF PIR (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
81 pir 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
95 tigr 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1692 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
16 PRINTS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
83 hssp 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3009 GeneDB_Ddiscoideum 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
163 RepBase 4.03 vrtrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3017 GeneDB_Bparapertussis 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
87 wormpep 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
151 Plasmodium_RoosLab 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3016 GeneDB_Bbronchiseptica 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
146 S. cerevisiae translated orfs 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
182 UCSC human draft genomic sequence (June 15 release) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
4 DDBJ (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
159 RepBase 4.03 plnrep.ref 4.0.0 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
105 zfin 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
190 TRRD 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
2094 cazy 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
22 GenBank 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
140 epd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3019 GeneDB_Styphi 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
145 C.elegans translated orfs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
162 RepBase 4.03 simple.ref 3.1 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
169 JGI/ORNL contigs 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
88 dictydb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
173 SCOP 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
793 Derisi Oligos 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
7 Swiss Prot (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3007 GeneDB_Scerevisiae 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
160 RepBase 4.03 pseudo.ref 1.0.5 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
91 swiss-2dpage 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
129 imgt/hla 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
123 taxon 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
100 yepd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
96 sgd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1092 LocusID 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
86 maizedb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
142 ORNL_grailexp_mrna 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
992 NCBI RefSeq 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3015 GeneDB_Tbrucei 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
147 TIGR mouse BAC ends 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
192 NCBI Malaria Genetics and Genome Project 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
99 gcrdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
11 General database Identifier (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
107 rebase 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
180 KEGG: Kyoto Encyclopedia of Genes and Genomes 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3026 SWALL 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
158 RepBase 4.03 mamrep.ref 5.2.2 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
492 Mouse BAC fingerprint map 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
177 Incyte 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
134 gdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
93 pdb 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3003 GO Process 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
167 Riethman lab. telomere sequences 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3021 SPTR 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
141 ORNL_genscan_mrna 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3023 TC 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
174 SMART 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
3020 GeneDB_Gmorsitans 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
139 rzpd 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
168 NCBI Reference Sequence (nrdb) 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1294 COG 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
1592 Schwartz Lab Optical Mapping Data 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
19 Unigene_44 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
183 ORNL GenScan gene predictions 2007-05-06
22:04:51.888548 1 1 1 1 1 0 1 1 1 3
171 Pfam-B 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
176 MEROPS 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
150 Plasmodium_Sanger 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
\.
Thanks in advance for any help you might provide ;-)
Cheers, Alberto
davila wrote:
> Thanks Steve !
>
> I will open the script and check it, however, is this a GUS plugin :
> "GUS::Supported::UnflattenBioperlFeatures::preprocess" ? if so, it is
> not available at $GUS_HOME or $PROJECT_HOME plugin directories:
>
> [davila1@kineto4 Supported]$ ls -lh $PROJECT_HOME/GUS/Supported/plugin/perl/
> total 668K
> -rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
> -rw-r--r-- 1 davila1 gus 12K May 3 17:12 CalculateTranslatedAASequences.pm
> -rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
> -rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
> -rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
> -rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
> -rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
> -rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
> -rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 InsertOntologyRelationshipType.pm
> -rw-r--r-- 1 davila1 gus 16K May 3 17:12
> InsertOntologyTermsAndRelationships.pm
> -rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
> -rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
> -rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
> -rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
> -rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
> -rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
> -rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
> -rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
> -rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
> -rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
> -rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
> drwxr-xr-x 3 davila1 gus 4.0K May 3 17:12 Test
>
> [davila1@kineto4 Supported]$ ls -lh $GUS_HOME/lib/perl/GUS/Supported/Plugin/
> total 668K
> -rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
> -rw-r--r-- 1 davila1 gus 12K May 3 17:12 CalculateTranslatedAASequences.pm
> -rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
> -rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
> -rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
> -rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
> -rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
> -rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
> -rw-r--r-- 1 davila1 gus 3.2K May 3 17:12 InsertOntologyRelationshipType.pm
> -rw-r--r-- 1 davila1 gus 16K May 3 17:12
> InsertOntologyTermsAndRelationships.pm
> -rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
> -rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
> -rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
> -rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
> -rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
> -rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
> -rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
> -rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
> -rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
> -rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
> -rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
> drwxr-xr-x 2 davila1 gus 4.0K May 3 17:12 Test
>
> This is the part of the
> "$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm" plugin
> originating the error:
>
> sub preprocessBioperlSeq {
> my ($self, $bioperlSeq) = @_;
> return unless $self->{bioperlSeqPreprocessor};
> my $class = $self->{bioperlSeqPreprocessor}->{class};
>
> eval {
> no strict "refs";
> eval "require $class";
> my $method = "${class}::preprocess";
> &$method($bioperlSeq); ### Line 63 originating the error #####
> };
>
> my $err = $@;
> if ($err) { die "Can't run bioperlSeq preprocessor method
> '${class}::preprocess'. Error:\n $err\n"; }
> }
>
> Where I can find "$bioperlSeq" ?
>
> Thanks, Alberto
>
>
>
> -----Mensagem original-----
> De: Steve Fischer [mailto:sfi...@pc...]
> Enviada: sex 11-mai-07 3:01
> Para: davila
> Cc: gus...@li...; mro...@cs...;
> cj...@fr...
> Assunto: Re: [GUSDEV] ISF error
>
> it looks as though it is trying to find the taxon of the sequence but is
> coming up with a null (see the method getTaxonId in the plugin).
>
> if the file contains all one species, you can provide that on the
> command line.
>
> otherwise, you'll need to look at the plugin code to see where in the
> files it is expecting to find that info and correct the files so that it
> is there.
>
> steve
>
> davila wrote:
> >
> > Hi Folks, could anyone help to debug this error ?
> >
> > ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> > /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> > --extDbRlsVer 159.0
> > Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=mydb
> > Fri May 11 13:20:31 2007 PLUGIN
> > GUS::Supported::Plugin::InsertSequenceFeatures
> > Fri May 11 13:20:31 2007 ARG algoinvo 1
> > Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
> > Fri May 11 13:20:31 2007 ARG comment
> > Fri May 11 13:20:31 2007 ARG commit 0
> > Fri May 11 13:20:31 2007 ARG debug 0
> > Fri May 11 13:20:31 2007 ARG defaultOrganism
> > Fri May 11 13:20:31 2007 ARG extDbName GenBank
> > Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
> > Fri May 11 13:20:31 2007 ARG fileFormat genbank
> > Fri May 11 13:20:31 2007 ARG gff2GroupTag
> > Fri May 11 13:20:31 2007 ARG group
> > Fri May 11 13:20:31 2007 ARG gusconfigfile
> > $GUS_HOME/config/gus.config
> > Fri May 11 13:20:31 2007 ARG handlerExternalDbs
> > Fri May 11 13:20:31 2007 ARG help
> > Fri May 11 13:20:31 2007 ARG helpHTML
> > Fri May 11 13:20:31 2007 ARG inputFileExtension
> > Fri May 11 13:20:31 2007 ARG inputFileOrDir
> > /home/davila1/lguyanensis.gb
> > Fri May 11 13:20:31 2007 ARG mapFile
> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> > Fri May 11 13:20:31 2007 ARG naSequenceSubclass
> > Fri May 11 13:20:31 2007 ARG organism
> > Fri May 11 13:20:31 2007 ARG project
> > Fri May 11 13:20:31 2007 ARG seqExtDbName
> > Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
> > Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
> > Fri May 11 13:20:31 2007 ARG seqSoTerm
> > Fri May 11 13:20:31 2007 ARG seqType
> > Fri May 11 13:20:31 2007 ARG soCvsVersion
> > Fri May 11 13:20:31 2007 ARG sqlVerbose 0
> > Fri May 11 13:20:31 2007 ARG testNumber
> > Fri May 11 13:20:31 2007 ARG user
> > Fri May 11 13:20:31 2007 ARG verbose 0
> > Fri May 11 13:20:31 2007 ARG veryVerbose 0
> > Fri May 11 13:20:31 2007 AlgInvocationId 61
> > Fri May 11 13:20:31 2007 COMMIT commit off
> > Fri May 11 13:20:31 2007 Processing file
> > '/home/davila1/lguyanensis.gb'...
> >
> > ERROR:
> > Attempting to get id from cache with null name at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> > 1103, <GEN32> line 65.
> >
> > STACK TRACE:
> > at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> > line 1103
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
> > 'taxon_id') called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 998
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 645
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 604
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 574
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 361
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
> > 'HASH(0x20628f0)') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> > eval {...} called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> >
> >
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
> >
> >
> > However, when I use --organism and --defaultOrganism the error changes:
> >
> > ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
> > /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> > --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
> > --defaultOrganism "Leishmania guyanensis" --verbose
> > Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=mydb
> > Fri May 11 13:21:54 2007 PLUGIN
> > GUS::Supported::Plugin::InsertSequenceFeatures
> > Fri May 11 13:21:54 2007 ARG algoinvo 1
> > Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
> > Fri May 11 13:21:54 2007 ARG comment
> > Fri May 11 13:21:54 2007 ARG commit 0
> > Fri May 11 13:21:54 2007 ARG debug 0
> > Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania
> > guyanensis
> > Fri May 11 13:21:54 2007 ARG extDbName GenBank
> > Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
> > Fri May 11 13:21:54 2007 ARG fileFormat genbank
> > Fri May 11 13:21:54 2007 ARG gff2GroupTag
> > Fri May 11 13:21:54 2007 ARG group
> > Fri May 11 13:21:54 2007 ARG gusconfigfile
> > $GUS_HOME/config/gus.config
> > Fri May 11 13:21:54 2007 ARG handlerExternalDbs
> > Fri May 11 13:21:54 2007 ARG help
> > Fri May 11 13:21:54 2007 ARG helpHTML
> > Fri May 11 13:21:54 2007 ARG inputFileExtension
> > Fri May 11 13:21:54 2007 ARG inputFileOrDir
> > /home/davila1/lguyanensis.gb
> > Fri May 11 13:21:54 2007 ARG mapFile
> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
> > Fri May 11 13:21:54 2007 ARG naSequenceSubclass
> > Fri May 11 13:21:54 2007 ARG organism Leishmania
> > guyanensis
> > Fri May 11 13:21:54 2007 ARG project
> > Fri May 11 13:21:54 2007 ARG seqExtDbName
> > Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
> > Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
> > Fri May 11 13:21:54 2007 ARG seqSoTerm
> > Fri May 11 13:21:54 2007 ARG seqType
> > Fri May 11 13:21:54 2007 ARG soCvsVersion
> > Fri May 11 13:21:54 2007 ARG sqlVerbose 0
> > Fri May 11 13:21:54 2007 ARG testNumber
> > Fri May 11 13:21:54 2007 ARG user
> > Fri May 11 13:21:54 2007 ARG verbose 1
> > Fri May 11 13:21:54 2007 ARG veryVerbose 0
> > Fri May 11 13:21:54 2007 AlgInvocationId 62
> > Fri May 11 13:21:54 2007 COMMIT commit off
> > Fri May 11 13:21:54 2007 Processing file
> > '/home/davila1/lguyanensis.gb'...
> >
> > ERROR:
> > Can't run bioperlSeq preprocessor method
> > 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
> >
> > ERROR:
> > Undefined subroutine
> > &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
> > $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
> > <GEN32> line 65.
> >
> > STACK TRACE:
> > at
> > /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
> > line 63
> > eval {...} called at
> > $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
> >
> >
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> > called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 365
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> > 'HASH(0x2062960)') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> > eval {...} called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> >
> >
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
> >
> >
> >
> > STACK TRACE:
> > at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
> >
> >
> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
> > 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
> > called at
> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 365
> >
> >
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
> > 'HASH(0x2062960)') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> > eval {...} called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> >
> >
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
> >
> >
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
> >
> > Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy
> > (*.dmp) file from May 11 2007, apparently it does not make a new load,
> > but updates the respective Sres tables, anyway such as the first run
> > the re-run of LoadTaxon provided these warnings:
> >
> > Fri May 11 12:42:27 2007 Merging taxons
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not
> > in database, skipping
> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not
> > in database, skipping
> >
> > What this exactly means ?
> >
> > The first time I ran LoadTaxon I got this log:
> >
> > tail LoadTaxon.log
> > Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
> > Mon May 7 00:07:39 2007 0 TaxonName entries deleted
> >
> > Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
> > Mon May 7 00:07:42 2007 RESULT 1
> > Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName: 485022
> > Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
> > Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
> > Mon May 7 00:07:47 2007 AlgInvocationId 7
> > Mon May 7 00:07:47 2007 COMMIT commit on
> >
> > The second time:
> >
> > tail LoadTaxon_new.log
> > Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
> > Fri May 11 13:07:51 2007 288 TaxonName entries deleted
> >
> > Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
> > Fri May 11 13:07:55 2007 RESULT 1
> > Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
> > Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
> > Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
> > Fri May 11 13:07:56 2007 AlgInvocationId 56
> > Fri May 11 13:07:56 2007 COMMIT commit on
> >
> > I just checked the sres.taxonname and it has Leishmania guyanensis there:
> >
> > SELECT
> >
> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
> > FROM "sres"."taxonname" WHERE
> > "name" = 'Leishmania guyanensis';
> > taxon_name_id | taxon_id | name |
> > unique_name_variant | name_class | modification_date |
> > row_project_id | row_alg_invocation_id
> >
> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
> > 369208 | 96595 | Leishmania guyanensis
> > | | scientific name | 2007-05-06 23:41:16.98889
> > | 1 | 7
> > (1 row)
> >
> > According to the log, it could be an
> > UnflattenBioperlFeatures::preprocess error too...
> >
> > Some of th GIs (L. guyanensis) I am trying to load with the ISF
> > pluging are:
> >
> > 104530485
> > 60280340
> > 110816091
> > 76577720
> > 76577719
> > 76577718
> >
> > Thanks for any help you might provide.
> >
> > Cheers, Alberto
> >
>
>
> ------------------------------------------------------------------------
>
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> ------------------------------------------------------------------------
>
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
--
Alberto M. R. Dávila, PhD
Kinetoplastid Biology and Disease (Biomed Central)
http://www.kinetoplastids.com
IAEA Collaborating Center for Bioinformatics and Animal Genomics
DBBM / Instituto Oswaldo Cruz / FIOCRUZ
Av. Brasil 4365
Rio de Janeiro, RJ, Brasil
CEP 21040-900
Email: da...@fi...
amr...@gm...
Phone: 55-21-3865-8229 / 3865-8206
Fax: 55-21-2590-3495
-------------------------------------------------
The BiowebDB consortium: http://www.biowebdb.org
|
|
From: Steve F. <sfi...@pc...> - 2007-05-18 16:16:34
|
alberto-
the code is trying to insert a database cross reference to HSSP. to do
this it must create rows in ExternalDatabase and ExternaDatabaseRelease.
the problem is that when it tries to insert a row into ExternalDatabase,
it is using a primary key (18) that is already in use in that table.
the first guesses are that:
- there is something wrong with the database mechanism (postgres) to
generate sequential primary keys
- somebody manually inserted a row into that table, using 18 as a
primary key, without incrementing the primary key generating mechanism
steve
Alberto Davila wrote:
> Hi folks !
>
> We managed to pass several errors with ISF but this one is a bit strange:
>
> [davila1@kineto4 log]$ ga
> GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
> /system/GUS/gus_home/config/genbank2gus.xml --inputFileOrDir
> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
> --defaultOrganism "Leishmania guyanensis" --verbose --soCvsVersion 1.45
> Fri May 18 12:42:57 2007 DSN dbi:Pg:dbname=protozoa
> Fri May 18 12:42:57 2007 PLUGIN
> GUS::Supported::Plugin::InsertSequenceFeatures
> Fri May 18 12:42:57 2007 ARG algoinvo 1
> Fri May 18 12:42:57 2007 ARG bioperlTreeOutput 0
> Fri May 18 12:42:57 2007 ARG comment
> Fri May 18 12:42:57 2007 ARG commit 0
> Fri May 18 12:42:57 2007 ARG debug 0
> Fri May 18 12:42:57 2007 ARG defaultOrganism Leishmania
> guyanensis
> Fri May 18 12:42:57 2007 ARG extDbName GenBank
> Fri May 18 12:42:57 2007 ARG extDbRlsVer 159.0
> Fri May 18 12:42:57 2007 ARG fileFormat genbank
> Fri May 18 12:42:57 2007 ARG gff2GroupTag
> Fri May 18 12:42:57 2007 ARG group
> Fri May 18 12:42:57 2007 ARG gusconfigfile
> /system/GUS/gus_home/config/gus.config
> Fri May 18 12:42:57 2007 ARG handlerExternalDbs
> Fri May 18 12:42:57 2007 ARG help
> Fri May 18 12:42:57 2007 ARG helpHTML
> Fri May 18 12:42:57 2007 ARG inputFileExtension
> Fri May 18 12:42:57 2007 ARG inputFileOrDir
> /home/davila1/lguyanensis.gb
> Fri May 18 12:42:57 2007 ARG mapFile
> /system/GUS/gus_home/config/genbank2gus.xml
> Fri May 18 12:42:57 2007 ARG naSequenceSubclass
> Fri May 18 12:42:57 2007 ARG organism Leishmania
> guyanensis
> Fri May 18 12:42:57 2007 ARG project
> Fri May 18 12:42:57 2007 ARG seqExtDbName
> Fri May 18 12:42:57 2007 ARG seqExtDbRlsVer
> Fri May 18 12:42:57 2007 ARG seqIdColumn source_id
> Fri May 18 12:42:57 2007 ARG seqSoTerm
> Fri May 18 12:42:57 2007 ARG seqType
> Fri May 18 12:42:57 2007 ARG soCvsVersion 1.45
> Fri May 18 12:42:57 2007 ARG sqlVerbose 0
> Fri May 18 12:42:57 2007 ARG testNumber
> Fri May 18 12:42:57 2007 ARG user
> Fri May 18 12:42:57 2007 ARG verbose 1
> Fri May 18 12:42:57 2007 ARG veryVerbose 0
> Fri May 18 12:42:57 2007 AlgInvocationId 83
> Fri May 18 12:42:57 2007 COMMIT commit off
> Fri May 18 12:42:58 2007 Processing file
> '/home/davila1/lguyanensis.gb'...
> DBD::Pg::st execute failed: ERROR: duplicate key violates unique
> constraint "pk_externaldatabase"
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.ExternalDatabase ( group_write, other_read,
> group_read, name, user_read, row_user_id, external_database_id,
> modification_date, other_write, row_alg_invocation_id, row_project_id,
> row_group_id, user_write )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
> Values: 1, 1, 1, HSSP, 1, 1, 18, 0, 83, 1, 1, 1 at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
> SRes.ExternalDataba...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
> '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write,
> other_...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
> 'HASH(0x30d4870)') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>
> GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 160
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 134
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 117
>
> GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 106
>
> GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
> 'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 1021
>
> GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 891
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 771
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 367
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HASH(0x2062a70)') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
>
> STACK TRACE:
> at /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
> SRes.ExternalDataba...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1e619d0)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x30dae70)', 'ARRAY(0x30daec0)',
> '\x{a} INSERT INTO SRes.ExternalDatabase ( group_write,
> other_...') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 673
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)',
> 'HASH(0x30d4870)') called at
> /system/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 620
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at /system/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>
> GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x30d4b00)')
> called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 160
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getExtDatabaseRlsId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 134
>
> GUS::Supported::SpecialCaseQualifierHandlers::_getDbXRefId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 117
>
> GUS::Supported::SpecialCaseQualifierHandlers::buildDbXRef('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HSSP:P07711') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/SpecialCaseQualifierHandlers.pm
> line 106
>
> GUS::Supported::SpecialCaseQualifierHandlers::dbXRef('GUS::Supported::SpecialCaseQualifierHandlers=HASH(0x10694f0)',
> 'db_xref', 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 1021
>
> GUS::Supported::Plugin::InsertSequenceFeatures::handleFeatureTag('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)',
> 'GUS::Supported::BioperlFeatMapper=HASH(0x2456250)',
> 'GUS::Model::DoTS::Transcript=HASH(0x2f3bc00)', 'db_xref') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 891
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x2d2e390)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x30cdbe0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 897
>
> GUS::Supported::Plugin::InsertSequenceFeatures::applyQualifiers('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::SeqFeature::Generic=HASH(0x3081dd0)') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 771
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'Bio::Seq::RichSeq=HASH(0x300b780)', 96, 171, 'undef') called at
> /system/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 367
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdda20)',
> 'HASH(0x2062a70)') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
> eval {...} called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /system/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
> 'ARRAY(0x505dd0)') called at /system/GUS/gus_home/bin/ga line 11
>
> This is my external_database table:
>
> -- PostgreSQL database dump
> --
>
> SET client_encoding = 'UTF8';
> SET standard_conforming_strings = off;
> SET check_function_bodies = false;
> SET client_min_messages = warning;
> SET escape_string_warning = off;
>
> SET search_path = sres, pg_catalog;
>
>
> COPY externaldatabase (external_database_id, name, modification_date,
> user_read, user_write, group_read, group_write, other_read,
> other_write, row_user_id, row_group_id, row_project_id,
> row_alg_invocation_id) FROM stdin;
> 164 RepBase 4.03 zebrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 106 maize-2dpage 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 2093 homstrad 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 89 mim 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1 assembly 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 154 RepBase 4.03 celrep.ref 4.0.4 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 82 mendel 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 185 RIKEN/FANTOM 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 292 Plasmodium_GSS 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 102 hsc-2dpage 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 2096 PRODOM 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 189 COMPEL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3010 GeneDB_Lmajor 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 2095 load 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 97 subtilist 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 90 mgd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 17 GSDB 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 92 aarhus/ghent-2dpage 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 8 Brookhaven Protein Data Bank (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 184 ORNL GRAILExp gene predictions 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 12 GenPept 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 692 Plasmodium_TIGR 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 144 flybase translated orfs 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 3008 GeneDB_Afumigatus 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 165 RepBase 4.03 humsub.ref 1.0.2 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 13 IMAGE 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 94 ecogene 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3024 GOA 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3011 GeneDB_Pberghei 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3018 GeneDB_Bpertussis 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 1392 CDD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3 EMBL Data Library (nrdb) 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 2097 PFAMA 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 172 URL 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 108 hiv 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 101 stygene 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3014 GeneDB_Tannulata 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 181 Signaling PAthway Database (SPAD) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 10 GenInfo Backbone Id (nrdb) 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 2092 dbSNP 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 78 embl 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 84 prosite 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3025 PubMed 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 6 Protein Research Foundation (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 928 GI 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 85 flybase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 14 EGAD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 126 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1792 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 156 RepBase 4.03 humrep.ref 7.0.6 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 152 TUBERCULIST 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3005 GOC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 392 EPCon 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1892 PID 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 98 eco2dbase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 104 transfac 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 293 Plasmodium_EST 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 127 sptrembl 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 130 imgt/ligm 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1292 RATMAP 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1192 ATCC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3001 GO Function 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 124 SWISS-PROT 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 1494 CDD-Pfam 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 143 NCBI genomic Homo Sapiens 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 18 DOTS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 133 estlib 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 161 RepBase 4.03 rodrep.ref 3.3.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 157 RepBase 4.03 invrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 1495 CDD-Smart 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 79 pfam 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 103 carbbank 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 191 Whitehead Institute/MIT Center for Genome Research Mouse RH
> Map 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1
> 1 1 3
> 155 RepBase 4.03 drorep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 125 PSEUDO 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3006 GeneDB_Spombe 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3022 PMID 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 153 RepBase 4.03 athrep.ref 4.0.5 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 122 SPTREMBL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 186 UCSC human draft genomic sequence (October 7 release)
> 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1
> 1 3
> 179 GeneMap 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 135 agis 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3013 GeneDB_Pfalciparum 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 170 Pfam expert 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 178 StemCellDB public 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 149 Bucan lab. mouse BAC ends 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 148 Prodom 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3012 GeneDB_Pchabaudi 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 128 pseudo 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 175 INTERPRO 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 80 MEDLINE 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 3002 GO Component 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 21 gss_human_bak.seq 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 1293 RGD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 9 Patents (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 15 BLOCKS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 37 swissprot 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 2 GenBank (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 20 dbEST 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 166 Demeter 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 5 NBRF PIR (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 81 pir 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 95 tigr 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1692 dbSTS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 16 PRINTS 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 83 hssp 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3009 GeneDB_Ddiscoideum 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 163 RepBase 4.03 vrtrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 3017 GeneDB_Bparapertussis 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 87 wormpep 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 151 Plasmodium_RoosLab 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3016 GeneDB_Bbronchiseptica 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 146 S. cerevisiae translated orfs 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 182 UCSC human draft genomic sequence (June 15 release)
> 2007-05-06 22:04:51.888548 1 1 1 1 1 0 1 1
> 1 3
> 4 DDBJ (nrdb) 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 159 RepBase 4.03 plnrep.ref 4.0.0 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 105 zfin 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 190 TRRD 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 2094 cazy 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 22 GenBank 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 140 epd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3019 GeneDB_Styphi 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 145 C.elegans translated orfs 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 162 RepBase 4.03 simple.ref 3.1 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 169 JGI/ORNL contigs 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 88 dictydb 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 173 SCOP 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 793 Derisi Oligos 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 7 Swiss Prot (nrdb) 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3007 GeneDB_Scerevisiae 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 160 RepBase 4.03 pseudo.ref 1.0.5 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 91 swiss-2dpage 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 129 imgt/hla 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 123 taxon 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 100 yepd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 96 sgd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1092 LocusID 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 86 maizedb 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 142 ORNL_grailexp_mrna 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 992 NCBI RefSeq 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 3015 GeneDB_Tbrucei 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 147 TIGR mouse BAC ends 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 192 NCBI Malaria Genetics and Genome Project 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 99 gcrdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 11 General database Identifier (nrdb) 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 107 rebase 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 180 KEGG: Kyoto Encyclopedia of Genes and Genomes 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 3026 SWALL 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 158 RepBase 4.03 mamrep.ref 5.2.2 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 492 Mouse BAC fingerprint map 2007-05-06 22:04:51.888548 1
> 1 1 1 1 0 1 1 1 3
> 177 Incyte 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 134 gdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 93 pdb 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3003 GO Process 2007-05-06 22:04:51.888548 1 1 1
> 1 1 0 1 1 1 3
> 167 Riethman lab. telomere sequences 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 3021 SPTR 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 141 ORNL_genscan_mrna 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 3023 TC 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 174 SMART 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 3020 GeneDB_Gmorsitans 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> 139 rzpd 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 168 NCBI Reference Sequence (nrdb) 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 1294 COG 2007-05-06 22:04:51.888548 1 1 1 1 1
> 0 1 1 1 3
> 1592 Schwartz Lab Optical Mapping Data 2007-05-06
> 22:04:51.888548 1 1 1 1 1 0 1 1 1 3
> 19 Unigene_44 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 183 ORNL GenScan gene predictions 2007-05-06 22:04:51.888548
> 1 1 1 1 1 0 1 1 1 3
> 171 Pfam-B 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 176 MEROPS 2007-05-06 22:04:51.888548 1 1 1 1
> 1 0 1 1 1 3
> 150 Plasmodium_Sanger 2007-05-06 22:04:51.888548 1 1
> 1 1 1 0 1 1 1 3
> \.
>
>
> Thanks in advance for any help you might provide ;-)
>
> Cheers, Alberto
>
>
>
>
> davila wrote:
>> Thanks Steve !
>>
>> I will open the script and check it, however, is this a GUS plugin :
>> "GUS::Supported::UnflattenBioperlFeatures::preprocess" ? if so, it is
>> not available at $GUS_HOME or $PROJECT_HOME plugin directories:
>>
>> [davila1@kineto4 Supported]$ ls -lh
>> $PROJECT_HOME/GUS/Supported/plugin/perl/
>> total 668K
>> -rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
>> -rw-r--r-- 1 davila1 gus 12K May 3 17:12
>> CalculateTranslatedAASequences.pm
>> -rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
>> -rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
>> -rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
>> -rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
>> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
>> -rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
>> -rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
>> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
>> -rw-r--r-- 1 davila1 gus 3.2K May 3 17:12
>> InsertOntologyRelationshipType.pm
>> -rw-r--r-- 1 davila1 gus 16K May 3 17:12
>> InsertOntologyTermsAndRelationships.pm
>> -rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
>> -rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
>> -rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
>> -rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
>> -rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
>> -rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
>> -rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
>> -rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
>> -rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
>> drwxr-xr-x 3 davila1 gus 4.0K May 3 17:12 Test
>>
>> [davila1@kineto4 Supported]$ ls -lh
>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/
>> total 668K
>> -rw-r--r-- 1 davila1 gus 3.3K May 3 17:12 CalculateAASequenceMolWt.pm
>> -rw-r--r-- 1 davila1 gus 12K May 3 17:12
>> CalculateTranslatedAASequences.pm
>> -rw-r--r-- 1 davila1 gus 38K May 3 17:12 dbEST.pm
>> -rw-r--r-- 1 davila1 gus 7.5K May 3 17:12 ExtractTranscriptSequences.pm
>> -rw-r--r-- 1 davila1 gus 28K May 3 17:12 InsertArrayDesignControl.pm
>> -rw-r--r-- 1 davila1 gus 18K May 3 17:12 InsertAssayControl.pm
>> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertBlastSimilarities.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 InsertContact.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertExternalDatabase.pm
>> -rw-r--r-- 1 davila1 gus 8.4K May 3 17:12 InsertExternalDatabaseRls.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Accession.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertGene2Go.pm
>> -rw-r--r-- 1 davila1 gus 37K May 3 17:12 InsertGeneOntologyAssoc.pm
>> -rw-r--r-- 1 davila1 gus 26K May 3 17:12 InsertGeneOntology.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertGOEvidenceCode.pm
>> -rw-r--r-- 1 davila1 gus 14K May 3 17:12 InsertHomoloGene.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertOntologyEntry.pm
>> -rw-r--r-- 1 davila1 gus 3.2K May 3 17:12
>> InsertOntologyRelationshipType.pm
>> -rw-r--r-- 1 davila1 gus 16K May 3 17:12
>> InsertOntologyTermsAndRelationships.pm
>> -rw-r--r-- 1 davila1 gus 3.1K May 3 17:12 InsertOntologyTermType.pm
>> -rw-r--r-- 1 davila1 gus 30K May 3 17:12 InsertRadAnalysis.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May 3 17:12 InsertReviewStatus.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May 3 17:12 InsertSecondaryStructure.pm
>> -rw-r--r-- 1 davila1 gus 41K May 3 17:12 InsertSequenceFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.2K May 3 17:12 InsertSequenceFeaturesUndo.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntologyNew.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May 3 17:12 InsertSequenceOntologyOBO.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 InsertSequenceOntology.pm
>> -rw-r--r-- 1 davila1 gus 7.1K May 3 17:12 InsertTandemRepeatFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.4K May 3 17:12 InsertTaxonAndTaxonName.pm
>> -rw-r--r-- 1 davila1 gus 55K May 3 17:12 LoadArrayDesign.pm
>> -rw-r--r-- 1 davila1 gus 46K May 3 17:12 LoadArrayResults.pm
>> -rw-r--r-- 1 davila1 gus 23K May 3 17:12 LoadFastaSequences.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May 3 17:12 LoadGusXml.pm
>> -rw-r--r-- 1 davila1 gus 25K May 3 17:12 LoadNRDB.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May 3 17:12 LoadRow.pm
>> -rw-r--r-- 1 davila1 gus 13K May 3 17:12 LoadTaxon.pm
>> drwxr-xr-x 2 davila1 gus 4.0K May 3 17:12 Test
>>
>> This is the part of the
>> "$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm" plugin
>> originating the error:
>>
>> sub preprocessBioperlSeq {
>> my ($self, $bioperlSeq) = @_;
>> return unless $self->{bioperlSeqPreprocessor};
>> my $class = $self->{bioperlSeqPreprocessor}->{class};
>>
>> eval {
>> no strict "refs";
>> eval "require $class";
>> my $method = "${class}::preprocess";
>> &$method($bioperlSeq); ### Line 63 originating the error #####
>> };
>>
>> my $err = $@;
>> if ($err) { die "Can't run bioperlSeq preprocessor method
>> '${class}::preprocess'. Error:\n $err\n"; }
>> }
>>
>> Where I can find "$bioperlSeq" ?
>>
>> Thanks, Alberto
>>
>>
>>
>> -----Mensagem original-----
>> De: Steve Fischer [mailto:sfi...@pc...]
>> Enviada: sex 11-mai-07 3:01
>> Para: davila
>> Cc: gus...@li...; mro...@cs...;
>> cj...@fr...
>> Assunto: Re: [GUSDEV] ISF error
>>
>> it looks as though it is trying to find the taxon of the sequence but is
>> coming up with a null (see the method getTaxonId in the plugin).
>>
>> if the file contains all one species, you can provide that on the
>> command line.
>>
>> otherwise, you'll need to look at the plugin code to see where in the
>> files it is expecting to find that info and correct the files so that it
>> is there.
>>
>> steve
>>
>> davila wrote:
>> >
>> > Hi Folks, could anyone help to debug this error ?
>> >
>> > ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>> > /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>> > --extDbRlsVer 159.0
>> > Fri May 11 13:20:31 2007 DSN dbi:Pg:dbname=mydb
>> > Fri May 11 13:20:31 2007 PLUGIN >
>> GUS::Supported::Plugin::InsertSequenceFeatures
>> > Fri May 11 13:20:31 2007 ARG algoinvo 1
>> > Fri May 11 13:20:31 2007 ARG bioperlTreeOutput 0
>> > Fri May 11 13:20:31 2007 ARG comment
>> > Fri May 11 13:20:31 2007 ARG commit 0
>> > Fri May 11 13:20:31 2007 ARG debug 0
>> > Fri May 11 13:20:31 2007 ARG defaultOrganism
>> > Fri May 11 13:20:31 2007 ARG extDbName GenBank
>> > Fri May 11 13:20:31 2007 ARG extDbRlsVer 159.0
>> > Fri May 11 13:20:31 2007 ARG fileFormat genbank
>> > Fri May 11 13:20:31 2007 ARG gff2GroupTag
>> > Fri May 11 13:20:31 2007 ARG group
>> > Fri May 11 13:20:31 2007 ARG gusconfigfile >
>> $GUS_HOME/config/gus.config
>> > Fri May 11 13:20:31 2007 ARG handlerExternalDbs
>> > Fri May 11 13:20:31 2007 ARG help
>> > Fri May 11 13:20:31 2007 ARG helpHTML
>> > Fri May 11 13:20:31 2007 ARG inputFileExtension
>> > Fri May 11 13:20:31 2007 ARG inputFileOrDir >
>> /home/davila1/lguyanensis.gb
>> > Fri May 11 13:20:31 2007 ARG mapFile
>> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>> > Fri May 11 13:20:31 2007 ARG naSequenceSubclass
>> > Fri May 11 13:20:31 2007 ARG organism
>> > Fri May 11 13:20:31 2007 ARG project
>> > Fri May 11 13:20:31 2007 ARG seqExtDbName
>> > Fri May 11 13:20:31 2007 ARG seqExtDbRlsVer
>> > Fri May 11 13:20:31 2007 ARG seqIdColumn source_id
>> > Fri May 11 13:20:31 2007 ARG seqSoTerm
>> > Fri May 11 13:20:31 2007 ARG seqType
>> > Fri May 11 13:20:31 2007 ARG soCvsVersion
>> > Fri May 11 13:20:31 2007 ARG sqlVerbose 0
>> > Fri May 11 13:20:31 2007 ARG testNumber
>> > Fri May 11 13:20:31 2007 ARG user
>> > Fri May 11 13:20:31 2007 ARG verbose 0
>> > Fri May 11 13:20:31 2007 ARG veryVerbose 0
>> > Fri May 11 13:20:31 2007 AlgInvocationId 61
>> > Fri May 11 13:20:31 2007 COMMIT commit off
>> > Fri May 11 13:20:31 2007 Processing file
>> > '/home/davila1/lguyanensis.gb'...
>> >
>> > ERROR:
>> > Attempting to get id from cache with null name at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line
>> > 1103, <GEN32> line 65.
>> >
>> > STACK TRACE:
>> > at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> > line 1103
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
>> > 'taxon_id') called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 998
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 645
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 604
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 574
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 361
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>
>> > 'HASH(0x20628f0)') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>> > eval {...} called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>> > >
>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>> >
>> >
>> > However, when I use --organism and --defaultOrganism the error
>> changes:
>> >
>> > ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>> > /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>> > --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
>> > --defaultOrganism "Leishmania guyanensis" --verbose
>> > Fri May 11 13:21:54 2007 DSN dbi:Pg:dbname=mydb
>> > Fri May 11 13:21:54 2007 PLUGIN >
>> GUS::Supported::Plugin::InsertSequenceFeatures
>> > Fri May 11 13:21:54 2007 ARG algoinvo 1
>> > Fri May 11 13:21:54 2007 ARG bioperlTreeOutput 0
>> > Fri May 11 13:21:54 2007 ARG comment
>> > Fri May 11 13:21:54 2007 ARG commit 0
>> > Fri May 11 13:21:54 2007 ARG debug 0
>> > Fri May 11 13:21:54 2007 ARG defaultOrganism Leishmania
>> > guyanensis
>> > Fri May 11 13:21:54 2007 ARG extDbName GenBank
>> > Fri May 11 13:21:54 2007 ARG extDbRlsVer 159.0
>> > Fri May 11 13:21:54 2007 ARG fileFormat genbank
>> > Fri May 11 13:21:54 2007 ARG gff2GroupTag
>> > Fri May 11 13:21:54 2007 ARG group
>> > Fri May 11 13:21:54 2007 ARG gusconfigfile >
>> $GUS_HOME/config/gus.config
>> > Fri May 11 13:21:54 2007 ARG handlerExternalDbs
>> > Fri May 11 13:21:54 2007 ARG help
>> > Fri May 11 13:21:54 2007 ARG helpHTML
>> > Fri May 11 13:21:54 2007 ARG inputFileExtension
>> > Fri May 11 13:21:54 2007 ARG inputFileOrDir >
>> /home/davila1/lguyanensis.gb
>> > Fri May 11 13:21:54 2007 ARG mapFile
>> > $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>> > Fri May 11 13:21:54 2007 ARG naSequenceSubclass
>> > Fri May 11 13:21:54 2007 ARG organism Leishmania
>> > guyanensis
>> > Fri May 11 13:21:54 2007 ARG project
>> > Fri May 11 13:21:54 2007 ARG seqExtDbName
>> > Fri May 11 13:21:54 2007 ARG seqExtDbRlsVer
>> > Fri May 11 13:21:54 2007 ARG seqIdColumn source_id
>> > Fri May 11 13:21:54 2007 ARG seqSoTerm
>> > Fri May 11 13:21:54 2007 ARG seqType
>> > Fri May 11 13:21:54 2007 ARG soCvsVersion
>> > Fri May 11 13:21:54 2007 ARG sqlVerbose 0
>> > Fri May 11 13:21:54 2007 ARG testNumber
>> > Fri May 11 13:21:54 2007 ARG user
>> > Fri May 11 13:21:54 2007 ARG verbose 1
>> > Fri May 11 13:21:54 2007 ARG veryVerbose 0
>> > Fri May 11 13:21:54 2007 AlgInvocationId 62
>> > Fri May 11 13:21:54 2007 COMMIT commit off
>> > Fri May 11 13:21:54 2007 Processing file
>> > '/home/davila1/lguyanensis.gb'...
>> >
>> > ERROR:
>> > Can't run bioperlSeq preprocessor method
>> > 'GUS::Supported::UnflattenBioperlFeatures::preprocess'. Error:
>> >
>> > ERROR:
>> > Undefined subroutine
>> > &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
>> > $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
>> > <GEN32> line 65.
>> >
>> > STACK TRACE:
>> > at
>> > /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
>> > line 63
>> > eval {...} called at
>> > $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
>> > >
>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>> > called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 365
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>
>> > 'HASH(0x2062960)') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>> > eval {...} called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>> > >
>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>> >
>> >
>> >
>> > STACK TRACE:
>> > at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
>> > >
>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>
>> > 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>> > called at
>> > $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>> line 365
>> > >
>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>
>> > 'HASH(0x2062960)') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>> > eval {...} called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>> > >
>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>> > $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>> > >
>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>
>> > 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>> >
>> > Today I re-ran the LoadTaxon plugin with a new version of the
>> Taxonomy
>> > (*.dmp) file from May 11 2007, apparently it does not make a new
>> load,
>> > but updates the respective Sres tables, anyway such as the first run
>> > the re-run of LoadTaxon provided these warnings:
>> >
>> > Fri May 11 12:42:27 2007 Merging taxons
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '12' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '30' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '37' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '46' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '67' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '76' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '77' not
>> > in database, skipping
>> > Fri May 11 12:42:27 2007 Doing merge and NCBI tax id '79' not
>> > in database, skipping
>> >
>> > What this exactly means ?
>> >
>> > The first time I ran LoadTaxon I got this log:
>> >
>> > tail LoadTaxon.log
>> > Mon May 7 00:07:35 2007 Deleting TaxonNames when redundant
>> > Mon May 7 00:07:39 2007 0 TaxonName entries deleted
>> >
>> > Mon May 7 00:07:42 2007 TIME 6653 sec (1:50:53)
>> > Mon May 7 00:07:42 2007 RESULT 1
>> > Mon May 7 00:07:47 2007 Rows Written SRes.TaxonName:
>> 485022
>> > Mon May 7 00:07:47 2007 Rows Written SRes.Taxon: 359527
>> > Mon May 7 00:07:47 2007 Rows Written SRes.GeneticCode: 18
>> > Mon May 7 00:07:47 2007 AlgInvocationId 7
>> > Mon May 7 00:07:47 2007 COMMIT commit on
>> >
>> > The second time:
>> >
>> > tail LoadTaxon_new.log
>> > Fri May 11 13:07:47 2007 Deleting TaxonNames when redundant
>> > Fri May 11 13:07:51 2007 288 TaxonName entries deleted
>> >
>> > Fri May 11 13:07:55 2007 TIME 1528 sec (0:25:28)
>> > Fri May 11 13:07:55 2007 RESULT 1
>> > Fri May 11 13:07:56 2007 Rows Written SRes.TaxonName: 4023
>> > Fri May 11 13:07:56 2007 Rows Written SRes.Taxon: 2263
>> > Fri May 11 13:07:56 2007 Rows Written SRes.GeneticCode: 0
>> > Fri May 11 13:07:56 2007 AlgInvocationId 56
>> > Fri May 11 13:07:56 2007 COMMIT commit on
>> >
>> > I just checked the sres.taxonname and it has Leishmania guyanensis
>> there:
>> >
>> > SELECT
>> >
>> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
>>
>> > FROM "sres"."taxonname" WHERE
>> > "name" = 'Leishmania guyanensis';
>> > taxon_name_id | taxon_id | name |
>> > unique_name_variant | name_class | modification_date |
>> > row_project_id | row_alg_invocation_id
>> >
>> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
>>
>> > 369208 | 96595 | Leishmania guyanensis
>> > | | scientific name | 2007-05-06 23:41:16.98889
>> > | 1 | 7
>> > (1 row)
>> >
>> > According to the log, it could be an
>> > UnflattenBioperlFeatures::preprocess error too...
>> >
>> > Some of th GIs (L. guyanensis) I am trying to load with the ISF
>> > pluging are:
>> >
>> > 104530485
>> > 60280340
>> > 110816091
>> > 76577720
>> > 76577719
>> > 76577718
>> >
>> > Thanks for any help you might provide.
>> >
>> > Cheers, Alberto
>> >
>>
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>>
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>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
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>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
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