Re: [GUSDEV] Gusdev-gusdev Digest, Vol 11, Issue 4

[Alberto D. <da...@io...>]

Thanks Michael,

I really loaded my taxon data first (exactly the same way you mention) , 
the problem appears to be related to a missing plugin... but of course I 
am not sure :-(

Could you kindly check if you have 
"GUS::Supported::UnflattenBioperlFeatures" as part of GUS 3.5 ?

Thanks


mro...@cs... wrote:
> Hi,
> 
> i think i had the same error when i loaded my sequences, it was because i
> had not loaded the taxon data first.
> 
> This is how i loaded the taxon files:
> 
> 
>   Loading Taxons: 11-27-2006 by MR
> 
>   Data downloaded from: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
> 
>   At: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
> 
>   "The NCBI taxonomy database contains the names of all organisms that
>    are represented in the genetic databases with at least one nucleotide
>    or protein sequence. Click on the tree if you want to browse the
>    taxonomic structure or retrieve sequence data for a particular group of
>    organisms"
> 
> 
>   I used: http://www.gusdb.org/wiki/index.php/Bootstrap%20data as a guide,
>   THIS IS FOR GUSDB 3.0 VERSION, WE ARE USING VERISON 3.5.
> 
>   The instructions were corrected as follow:
> 
>   ga GUS::Supported::Plugin::LoadTaxon --gencode ~/taxon/11-27-
>   2006/gencode.dmp --names ~/taxon/11-27-2006/names.dmp --nodes ~/taxon/11-
>   27-2006/nodes.dmp --merged ~/taxon/11-27-2006/merged.dmp --commit
> 
> 
> 
>   For a manual loading to mySql see -->
>   http://linnaeus.zoology.gla.ac.uk/~rpage/iphylo/projects/3/
> 
> 
>   Mon Nov 27 13:38:38 2006        Doing merge and NCBI tax id '413065'
>   not   in database, skipping
>   Mon Nov 27 13:38:38 2006        Updating and inserting SRes.GeneticCode
> 
>   Mon Nov 27 13:53:12 2006        Processed ncbi_tax_id : 49833
>   Mon Nov 27 13:53:12 2006        Processed ncbi_tax_id : 155113
> 
>   Mon Nov 27 14:56:10 2006        Processed ncbi_tax_id : 83469
>   Mon Nov 27 14:56:10 2006        Processed ncbi_tax_id : 195787
> 
>   this is more clear:
>   ga GUS::Supported::Plugin::LoadTaxon
>   --gencode ~/taxon/11-27-2006/gencode.dmp
>   --names   ~/taxon/11-27-2006/names.dmp
>   --nodes   ~/taxon/11-27-2006/nodes.dmp
>   --merged  ~/taxon/11-27-2006/merged.dmp --commit
> 
> 
> 
> Hope it helps
> 
> 
> Michael Robinson
> Bioinformatics Research Group (Biorg)
> Florida International University
> ECS 254
> Miami, Florida, USA 33199
> 
> 
> 
> 
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>> Today's Topics:
>>
>>    1. Re: ISF error (Steve Fischer)
>>    2. RES:  ISF error (davila)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 11 May 2007 14:01:47 -0400
>> From: Steve Fischer <sfi...@pc...>
>> Subject: Re: [GUSDEV] ISF error
>> To: davila <da...@io...>
>> Cc: gus...@li..., mro...@cs...,
>> 	cj...@fr...
>> Message-ID: <464...@pc...>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> it looks as though it is trying to find the taxon of the sequence but is
>> coming up with a null (see the method getTaxonId in the plugin).
>>
>> if the file contains all one species, you can provide that on the
>> command line.
>>
>> otherwise, you'll need to look at the plugin code to see where in the
>> files it is expecting to find that info and correct the files so that it
>> is there.
>>
>> steve
>>
>> davila wrote:
>>> Hi Folks, could anyone help to debug this error  ?
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>>> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>>> --extDbRlsVer 159.0
>>> Fri May 11 13:20:31 2007        DSN     dbi:Pg:dbname=mydb
>>> Fri May 11 13:20:31 2007        PLUGIN
>>> GUS::Supported::Plugin::InsertSequenceFeatures
>>> Fri May 11 13:20:31 2007        ARG     algoinvo        1
>>> Fri May 11 13:20:31 2007        ARG     bioperlTreeOutput       0
>>> Fri May 11 13:20:31 2007        ARG     comment
>>> Fri May 11 13:20:31 2007        ARG     commit  0
>>> Fri May 11 13:20:31 2007        ARG     debug   0
>>> Fri May 11 13:20:31 2007        ARG     defaultOrganism
>>> Fri May 11 13:20:31 2007        ARG     extDbName       GenBank
>>> Fri May 11 13:20:31 2007        ARG     extDbRlsVer     159.0
>>> Fri May 11 13:20:31 2007        ARG     fileFormat      genbank
>>> Fri May 11 13:20:31 2007        ARG     gff2GroupTag
>>> Fri May 11 13:20:31 2007        ARG     group
>>> Fri May 11 13:20:31 2007        ARG     gusconfigfile
>>> $GUS_HOME/config/gus.config
>>> Fri May 11 13:20:31 2007        ARG     handlerExternalDbs
>>> Fri May 11 13:20:31 2007        ARG     help
>>> Fri May 11 13:20:31 2007        ARG     helpHTML
>>> Fri May 11 13:20:31 2007        ARG     inputFileExtension
>>> Fri May 11 13:20:31 2007        ARG     inputFileOrDir
>>> /home/davila1/lguyanensis.gb
>>> Fri May 11 13:20:31 2007        ARG     mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>>> Fri May 11 13:20:31 2007        ARG     naSequenceSubclass
>>> Fri May 11 13:20:31 2007        ARG     organism
>>> Fri May 11 13:20:31 2007        ARG     project
>>> Fri May 11 13:20:31 2007        ARG     seqExtDbName
>>> Fri May 11 13:20:31 2007        ARG     seqExtDbRlsVer
>>> Fri May 11 13:20:31 2007        ARG     seqIdColumn     source_id
>>> Fri May 11 13:20:31 2007        ARG     seqSoTerm
>>> Fri May 11 13:20:31 2007        ARG     seqType
>>> Fri May 11 13:20:31 2007        ARG     soCvsVersion
>>> Fri May 11 13:20:31 2007        ARG     sqlVerbose      0
>>> Fri May 11 13:20:31 2007        ARG     testNumber
>>> Fri May 11 13:20:31 2007        ARG     user
>>> Fri May 11 13:20:31 2007        ARG     verbose 0
>>> Fri May 11 13:20:31 2007        ARG     veryVerbose     0
>>> Fri May 11 13:20:31 2007        AlgInvocationId 61
>>> Fri May 11 13:20:31 2007        COMMIT  commit off
>>> Fri May 11 13:20:31 2007        Processing file
>>> '/home/davila1/lguyanensis.gb'...
>>>
>>> ERROR:
>>> Attempting to get id from cache with null name at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 1103, <GEN32> line 65.
>>>
>>> STACK TRACE:
>>>  at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>>> line 1103
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
>>> 'taxon_id') called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 998
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 645
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 604
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 574
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 361
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'HASH(0x20628f0)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>>
>>> However, when I use --organism and --defaultOrganism the error changes:
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>>> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>>> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
>>> --defaultOrganism "Leishmania guyanensis" --verbose
>>> Fri May 11 13:21:54 2007        DSN     dbi:Pg:dbname=mydb
>>> Fri May 11 13:21:54 2007        PLUGIN
>>> GUS::Supported::Plugin::InsertSequenceFeatures
>>> Fri May 11 13:21:54 2007        ARG     algoinvo        1
>>> Fri May 11 13:21:54 2007        ARG     bioperlTreeOutput       0
>>> Fri May 11 13:21:54 2007        ARG     comment
>>> Fri May 11 13:21:54 2007        ARG     commit  0
>>> Fri May 11 13:21:54 2007        ARG     debug   0
>>> Fri May 11 13:21:54 2007        ARG     defaultOrganism Leishmania
>>> guyanensis
>>> Fri May 11 13:21:54 2007        ARG     extDbName       GenBank
>>> Fri May 11 13:21:54 2007        ARG     extDbRlsVer     159.0
>>> Fri May 11 13:21:54 2007        ARG     fileFormat      genbank
>>> Fri May 11 13:21:54 2007        ARG     gff2GroupTag
>>> Fri May 11 13:21:54 2007        ARG     group
>>> Fri May 11 13:21:54 2007        ARG     gusconfigfile
>>> $GUS_HOME/config/gus.config
>>> Fri May 11 13:21:54 2007        ARG     handlerExternalDbs
>>> Fri May 11 13:21:54 2007        ARG     help
>>> Fri May 11 13:21:54 2007        ARG     helpHTML
>>> Fri May 11 13:21:54 2007        ARG     inputFileExtension
>>> Fri May 11 13:21:54 2007        ARG     inputFileOrDir
>>> /home/davila1/lguyanensis.gb
>>> Fri May 11 13:21:54 2007        ARG     mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>>> Fri May 11 13:21:54 2007        ARG     naSequenceSubclass
>>> Fri May 11 13:21:54 2007        ARG     organism        Leishmania
>>> guyanensis
>>> Fri May 11 13:21:54 2007        ARG     project
>>> Fri May 11 13:21:54 2007        ARG     seqExtDbName
>>> Fri May 11 13:21:54 2007        ARG     seqExtDbRlsVer
>>> Fri May 11 13:21:54 2007        ARG     seqIdColumn     source_id
>>> Fri May 11 13:21:54 2007        ARG     seqSoTerm
>>> Fri May 11 13:21:54 2007        ARG     seqType
>>> Fri May 11 13:21:54 2007        ARG     soCvsVersion
>>> Fri May 11 13:21:54 2007        ARG     sqlVerbose      0
>>> Fri May 11 13:21:54 2007        ARG     testNumber
>>> Fri May 11 13:21:54 2007        ARG     user
>>> Fri May 11 13:21:54 2007        ARG     verbose 1
>>> Fri May 11 13:21:54 2007        ARG     veryVerbose     0
>>> Fri May 11 13:21:54 2007        AlgInvocationId 62
>>> Fri May 11 13:21:54 2007        COMMIT  commit off
>>> Fri May 11 13:21:54 2007        Processing file
>>> '/home/davila1/lguyanensis.gb'...
>>>
>>> ERROR:
>>> Can't run bioperlSeq preprocessor method
>>> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'.  Error:
>>>
>>> ERROR:
>>> Undefined subroutine
>>> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
>>> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
>>> <GEN32> line 65.
>>>
>>> STACK TRACE:
>>>  at
>>> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
>>> line 63
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
>>>
>>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>>> called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 365
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>> 'HASH(0x2062960)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>>
>>>
>>> STACK TRACE:
>>>  at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
>>>
>>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>>> called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 365
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>> 'HASH(0x2062960)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>> Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy
>>> (*.dmp) file from May 11 2007, apparently it does not make a new load,
>>> but updates the respective Sres tables, anyway such as the first run
>>> the re-run of LoadTaxon provided these warnings:
>>>
>>> Fri May 11 12:42:27 2007        Merging taxons
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '12' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '30' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '37' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '46' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '67' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '76' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '77' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '79' not
>>> in database, skipping
>>>
>>> What this exactly means ?
>>>
>>> The first time I ran LoadTaxon I got this log:
>>>
>>> tail LoadTaxon.log
>>> Mon May  7 00:07:35 2007        Deleting TaxonNames when redundant
>>> Mon May  7 00:07:39 2007        0 TaxonName entries deleted
>>>
>>> Mon May  7 00:07:42 2007        TIME    6653 sec  (1:50:53)
>>> Mon May  7 00:07:42 2007        RESULT  1
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.TaxonName: 485022
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.Taxon: 359527
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.GeneticCode: 18
>>> Mon May  7 00:07:47 2007        AlgInvocationId 7
>>> Mon May  7 00:07:47 2007        COMMIT  commit on
>>>
>>> The second time:
>>>
>>> tail LoadTaxon_new.log
>>> Fri May 11 13:07:47 2007        Deleting TaxonNames when redundant
>>> Fri May 11 13:07:51 2007        288 TaxonName entries deleted
>>>
>>> Fri May 11 13:07:55 2007        TIME    1528 sec  (0:25:28)
>>> Fri May 11 13:07:55 2007        RESULT  1
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.TaxonName: 4023
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.Taxon: 2263
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.GeneticCode: 0
>>> Fri May 11 13:07:56 2007        AlgInvocationId 56
>>> Fri May 11 13:07:56 2007        COMMIT  commit on
>>>
>>> I just checked the sres.taxonname and it has Leishmania guyanensis
>>> there:
>>>
>>> SELECT
>>> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
>>> FROM "sres"."taxonname" WHERE
>>> "name" = 'Leishmania guyanensis';
>>>  taxon_name_id | taxon_id |         name          |
>>> unique_name_variant |   name_class    |     modification_date     |
>>> row_project_id | row_alg_invocation_id
>>> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
>>>         369208 |    96595 | Leishmania guyanensis
>>> |                     | scientific name | 2007-05-06 23:41:16.98889
>>> |              1 |                     7
>>> (1 row)
>>>
>>> According to the log, it could be an
>>> UnflattenBioperlFeatures::preprocess error too...
>>>
>>> Some of th GIs (L. guyanensis) I am trying to load with the ISF
>>> pluging are:
>>>
>>> 104530485
>>> 60280340
>>> 110816091
>>> 76577720
>>> 76577719
>>> 76577718
>>>
>>> Thanks for any help you might provide.
>>>
>>> Cheers, Alberto
>>>
>>> ------------------------------------------------------------------------
>>>
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>>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Sat, 12 May 2007 13:35:16 -0300
>> From: "davila" <da...@io...>
>> Subject: [GUSDEV] RES:  ISF error
>> To: "Steve Fischer" <sfi...@pc...>
>> Cc: gus...@li..., mro...@cs...,
>> 	pa...@ug...,	Felipe Liberman <fl...@io...>, cj...@fr...
>> Message-ID:
>> 	<620...@be...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Thanks Steve !
>>
>> I will open the script and check it, however, is this a GUS plugin :
>> "GUS::Supported::UnflattenBioperlFeatures::preprocess" ? if so, it is not
>> available at $GUS_HOME or $PROJECT_HOME plugin directories:
>>
>> [davila1@kineto4 Supported]$ ls -lh
>> $PROJECT_HOME/GUS/Supported/plugin/perl/
>> total 668K
>> -rw-r--r-- 1 davila1 gus 3.3K May  3 17:12 CalculateAASequenceMolWt.pm
>> -rw-r--r-- 1 davila1 gus  12K May  3 17:12
>> CalculateTranslatedAASequences.pm
>> -rw-r--r-- 1 davila1 gus  38K May  3 17:12 dbEST.pm
>> -rw-r--r-- 1 davila1 gus 7.5K May  3 17:12 ExtractTranscriptSequences.pm
>> -rw-r--r-- 1 davila1 gus  28K May  3 17:12 InsertArrayDesignControl.pm
>> -rw-r--r-- 1 davila1 gus  18K May  3 17:12 InsertAssayControl.pm
>> -rw-r--r-- 1 davila1 gus  26K May  3 17:12 InsertBlastSimilarities.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May  3 17:12 InsertContact.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May  3 17:12 InsertExternalDatabase.pm
>> -rw-r--r-- 1 davila1 gus 8.4K May  3 17:12 InsertExternalDatabaseRls.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertGene2Accession.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertGene2Go.pm
>> -rw-r--r-- 1 davila1 gus  37K May  3 17:12 InsertGeneOntologyAssoc.pm
>> -rw-r--r-- 1 davila1 gus  26K May  3 17:12 InsertGeneOntology.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May  3 17:12 InsertGOEvidenceCode.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertHomoloGene.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May  3 17:12 InsertOntologyEntry.pm
>> -rw-r--r-- 1 davila1 gus 3.2K May  3 17:12
>> InsertOntologyRelationshipType.pm
>> -rw-r--r-- 1 davila1 gus  16K May  3 17:12
>> InsertOntologyTermsAndRelationships.pm
>> -rw-r--r-- 1 davila1 gus 3.1K May  3 17:12 InsertOntologyTermType.pm
>> -rw-r--r-- 1 davila1 gus  30K May  3 17:12 InsertRadAnalysis.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May  3 17:12 InsertReviewStatus.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May  3 17:12 InsertSecondaryStructure.pm
>> -rw-r--r-- 1 davila1 gus  41K May  3 17:12 InsertSequenceFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.2K May  3 17:12 InsertSequenceFeaturesUndo.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 InsertSequenceOntologyNew.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May  3 17:12 InsertSequenceOntologyOBO.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 InsertSequenceOntology.pm
>> -rw-r--r-- 1 davila1 gus 7.1K May  3 17:12 InsertTandemRepeatFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.4K May  3 17:12 InsertTaxonAndTaxonName.pm
>> -rw-r--r-- 1 davila1 gus  55K May  3 17:12 LoadArrayDesign.pm
>> -rw-r--r-- 1 davila1 gus  46K May  3 17:12 LoadArrayResults.pm
>> -rw-r--r-- 1 davila1 gus  23K May  3 17:12 LoadFastaSequences.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May  3 17:12 LoadGusXml.pm
>> -rw-r--r-- 1 davila1 gus  25K May  3 17:12 LoadNRDB.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 LoadRow.pm
>> -rw-r--r-- 1 davila1 gus  13K May  3 17:12 LoadTaxon.pm
>> drwxr-xr-x 3 davila1 gus 4.0K May  3 17:12 Test
>>
>> [davila1@kineto4 Supported]$ ls -lh
>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/
>> total 668K
>> -rw-r--r-- 1 davila1 gus 3.3K May  3 17:12 CalculateAASequenceMolWt.pm
>> -rw-r--r-- 1 davila1 gus  12K May  3 17:12
>> CalculateTranslatedAASequences.pm
>> -rw-r--r-- 1 davila1 gus  38K May  3 17:12 dbEST.pm
>> -rw-r--r-- 1 davila1 gus 7.5K May  3 17:12 ExtractTranscriptSequences.pm
>> -rw-r--r-- 1 davila1 gus  28K May  3 17:12 InsertArrayDesignControl.pm
>> -rw-r--r-- 1 davila1 gus  18K May  3 17:12 InsertAssayControl.pm
>> -rw-r--r-- 1 davila1 gus  26K May  3 17:12 InsertBlastSimilarities.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May  3 17:12 InsertContact.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May  3 17:12 InsertExternalDatabase.pm
>> -rw-r--r-- 1 davila1 gus 8.4K May  3 17:12 InsertExternalDatabaseRls.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertGene2Accession.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertGene2Go.pm
>> -rw-r--r-- 1 davila1 gus  37K May  3 17:12 InsertGeneOntologyAssoc.pm
>> -rw-r--r-- 1 davila1 gus  26K May  3 17:12 InsertGeneOntology.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May  3 17:12 InsertGOEvidenceCode.pm
>> -rw-r--r-- 1 davila1 gus  14K May  3 17:12 InsertHomoloGene.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May  3 17:12 InsertOntologyEntry.pm
>> -rw-r--r-- 1 davila1 gus 3.2K May  3 17:12
>> InsertOntologyRelationshipType.pm
>> -rw-r--r-- 1 davila1 gus  16K May  3 17:12
>> InsertOntologyTermsAndRelationships.pm
>> -rw-r--r-- 1 davila1 gus 3.1K May  3 17:12 InsertOntologyTermType.pm
>> -rw-r--r-- 1 davila1 gus  30K May  3 17:12 InsertRadAnalysis.pm
>> -rw-r--r-- 1 davila1 gus 4.1K May  3 17:12 InsertReviewStatus.pm
>> -rw-r--r-- 1 davila1 gus 9.5K May  3 17:12 InsertSecondaryStructure.pm
>> -rw-r--r-- 1 davila1 gus  41K May  3 17:12 InsertSequenceFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.2K May  3 17:12 InsertSequenceFeaturesUndo.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 InsertSequenceOntologyNew.pm
>> -rw-r--r-- 1 davila1 gus 4.2K May  3 17:12 InsertSequenceOntologyOBO.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 InsertSequenceOntology.pm
>> -rw-r--r-- 1 davila1 gus 7.1K May  3 17:12 InsertTandemRepeatFeatures.pm
>> -rw-r--r-- 1 davila1 gus 6.4K May  3 17:12 InsertTaxonAndTaxonName.pm
>> -rw-r--r-- 1 davila1 gus  55K May  3 17:12 LoadArrayDesign.pm
>> -rw-r--r-- 1 davila1 gus  46K May  3 17:12 LoadArrayResults.pm
>> -rw-r--r-- 1 davila1 gus  23K May  3 17:12 LoadFastaSequences.pm
>> -rw-r--r-- 1 davila1 gus 5.0K May  3 17:12 LoadGusXml.pm
>> -rw-r--r-- 1 davila1 gus  25K May  3 17:12 LoadNRDB.pm
>> -rw-r--r-- 1 davila1 gus 4.3K May  3 17:12 LoadRow.pm
>> -rw-r--r-- 1 davila1 gus  13K May  3 17:12 LoadTaxon.pm
>> drwxr-xr-x 2 davila1 gus 4.0K May  3 17:12 Test
>>
>> This is the part of the
>> "$GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm" plugin
>> originating the error:
>>
>> sub preprocessBioperlSeq {
>>   my ($self, $bioperlSeq) = @_;
>>   return unless $self->{bioperlSeqPreprocessor};
>>   my $class = $self->{bioperlSeqPreprocessor}->{class};
>>
>>   eval {
>>     no strict "refs";
>>     eval "require $class";
>>     my $method = "${class}::preprocess";
>>     &$method($bioperlSeq); ###  Line 63 originating the error #####
>>   };
>>
>>   my $err = $@;
>>   if ($err) { die "Can't run bioperlSeq preprocessor method
>> '${class}::preprocess'.  Error:\n $err\n"; }
>> }
>>
>> Where I can find "$bioperlSeq" ?
>>
>> Thanks, Alberto
>>
>>
>>
>> -----Mensagem original-----
>> De: Steve Fischer [mailto:sfi...@pc...]
>> Enviada: sex 11-mai-07 3:01
>> Para: davila
>> Cc: gus...@li...; mro...@cs...;
>> cj...@fr...
>> Assunto: Re: [GUSDEV] ISF error
>>
>> it looks as though it is trying to find the taxon of the sequence but is
>> coming up with a null (see the method getTaxonId in the plugin).
>>
>> if the file contains all one species, you can provide that on the
>> command line.
>>
>> otherwise, you'll need to look at the plugin code to see where in the
>> files it is expecting to find that info and correct the files so that it
>> is there.
>>
>> steve
>>
>> davila wrote:
>>> Hi Folks, could anyone help to debug this error  ?
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>>> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>>> --extDbRlsVer 159.0
>>> Fri May 11 13:20:31 2007        DSN     dbi:Pg:dbname=mydb
>>> Fri May 11 13:20:31 2007        PLUGIN
>>> GUS::Supported::Plugin::InsertSequenceFeatures
>>> Fri May 11 13:20:31 2007        ARG     algoinvo        1
>>> Fri May 11 13:20:31 2007        ARG     bioperlTreeOutput       0
>>> Fri May 11 13:20:31 2007        ARG     comment
>>> Fri May 11 13:20:31 2007        ARG     commit  0
>>> Fri May 11 13:20:31 2007        ARG     debug   0
>>> Fri May 11 13:20:31 2007        ARG     defaultOrganism
>>> Fri May 11 13:20:31 2007        ARG     extDbName       GenBank
>>> Fri May 11 13:20:31 2007        ARG     extDbRlsVer     159.0
>>> Fri May 11 13:20:31 2007        ARG     fileFormat      genbank
>>> Fri May 11 13:20:31 2007        ARG     gff2GroupTag
>>> Fri May 11 13:20:31 2007        ARG     group
>>> Fri May 11 13:20:31 2007        ARG     gusconfigfile
>>> $GUS_HOME/config/gus.config
>>> Fri May 11 13:20:31 2007        ARG     handlerExternalDbs
>>> Fri May 11 13:20:31 2007        ARG     help
>>> Fri May 11 13:20:31 2007        ARG     helpHTML
>>> Fri May 11 13:20:31 2007        ARG     inputFileExtension
>>> Fri May 11 13:20:31 2007        ARG     inputFileOrDir
>>> /home/davila1/lguyanensis.gb
>>> Fri May 11 13:20:31 2007        ARG     mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>>> Fri May 11 13:20:31 2007        ARG     naSequenceSubclass
>>> Fri May 11 13:20:31 2007        ARG     organism
>>> Fri May 11 13:20:31 2007        ARG     project
>>> Fri May 11 13:20:31 2007        ARG     seqExtDbName
>>> Fri May 11 13:20:31 2007        ARG     seqExtDbRlsVer
>>> Fri May 11 13:20:31 2007        ARG     seqIdColumn     source_id
>>> Fri May 11 13:20:31 2007        ARG     seqSoTerm
>>> Fri May 11 13:20:31 2007        ARG     seqType
>>> Fri May 11 13:20:31 2007        ARG     soCvsVersion
>>> Fri May 11 13:20:31 2007        ARG     sqlVerbose      0
>>> Fri May 11 13:20:31 2007        ARG     testNumber
>>> Fri May 11 13:20:31 2007        ARG     user
>>> Fri May 11 13:20:31 2007        ARG     verbose 0
>>> Fri May 11 13:20:31 2007        ARG     veryVerbose     0
>>> Fri May 11 13:20:31 2007        AlgInvocationId 61
>>> Fri May 11 13:20:31 2007        COMMIT  commit off
>>> Fri May 11 13:20:31 2007        Processing file
>>> '/home/davila1/lguyanensis.gb'...
>>>
>>> ERROR:
>>> Attempting to get id from cache with null name at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 1103, <GEN32> line 65.
>>>
>>> STACK TRACE:
>>>  at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>>> line 1103
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'taxonNameCache', 'undef', 'GUS::Model::SRes::TaxonName', 'name',
>>> 'taxon_id') called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 998
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)') called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 645
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 604
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 574
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe130)', 171) called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 361
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd7f0)',
>>> 'HASH(0x20628f0)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>>
>>> However, when I use --organism and --defaultOrganism the error changes:
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml --inputFileOrDir
>>> /home/davila1/lguyanensis.gb --fileFormat genbank --extDbName GenBank
>>> --extDbRlsVer 159.0 --organism "Leishmania guyanensis"
>>> --defaultOrganism "Leishmania guyanensis" --verbose
>>> Fri May 11 13:21:54 2007        DSN     dbi:Pg:dbname=mydb
>>> Fri May 11 13:21:54 2007        PLUGIN
>>> GUS::Supported::Plugin::InsertSequenceFeatures
>>> Fri May 11 13:21:54 2007        ARG     algoinvo        1
>>> Fri May 11 13:21:54 2007        ARG     bioperlTreeOutput       0
>>> Fri May 11 13:21:54 2007        ARG     comment
>>> Fri May 11 13:21:54 2007        ARG     commit  0
>>> Fri May 11 13:21:54 2007        ARG     debug   0
>>> Fri May 11 13:21:54 2007        ARG     defaultOrganism Leishmania
>>> guyanensis
>>> Fri May 11 13:21:54 2007        ARG     extDbName       GenBank
>>> Fri May 11 13:21:54 2007        ARG     extDbRlsVer     159.0
>>> Fri May 11 13:21:54 2007        ARG     fileFormat      genbank
>>> Fri May 11 13:21:54 2007        ARG     gff2GroupTag
>>> Fri May 11 13:21:54 2007        ARG     group
>>> Fri May 11 13:21:54 2007        ARG     gusconfigfile
>>> $GUS_HOME/config/gus.config
>>> Fri May 11 13:21:54 2007        ARG     handlerExternalDbs
>>> Fri May 11 13:21:54 2007        ARG     help
>>> Fri May 11 13:21:54 2007        ARG     helpHTML
>>> Fri May 11 13:21:54 2007        ARG     inputFileExtension
>>> Fri May 11 13:21:54 2007        ARG     inputFileOrDir
>>> /home/davila1/lguyanensis.gb
>>> Fri May 11 13:21:54 2007        ARG     mapFile
>>> $PROJECT_HOME/GUS/Supported/config/genbank2gus.xml
>>> Fri May 11 13:21:54 2007        ARG     naSequenceSubclass
>>> Fri May 11 13:21:54 2007        ARG     organism        Leishmania
>>> guyanensis
>>> Fri May 11 13:21:54 2007        ARG     project
>>> Fri May 11 13:21:54 2007        ARG     seqExtDbName
>>> Fri May 11 13:21:54 2007        ARG     seqExtDbRlsVer
>>> Fri May 11 13:21:54 2007        ARG     seqIdColumn     source_id
>>> Fri May 11 13:21:54 2007        ARG     seqSoTerm
>>> Fri May 11 13:21:54 2007        ARG     seqType
>>> Fri May 11 13:21:54 2007        ARG     soCvsVersion
>>> Fri May 11 13:21:54 2007        ARG     sqlVerbose      0
>>> Fri May 11 13:21:54 2007        ARG     testNumber
>>> Fri May 11 13:21:54 2007        ARG     user
>>> Fri May 11 13:21:54 2007        ARG     verbose 1
>>> Fri May 11 13:21:54 2007        ARG     veryVerbose     0
>>> Fri May 11 13:21:54 2007        AlgInvocationId 62
>>> Fri May 11 13:21:54 2007        COMMIT  commit off
>>> Fri May 11 13:21:54 2007        Processing file
>>> '/home/davila1/lguyanensis.gb'...
>>>
>>> ERROR:
>>> Can't run bioperlSeq preprocessor method
>>> 'GUS::Supported::UnflattenBioperlFeatures::preprocess'.  Error:
>>>
>>> ERROR:
>>> Undefined subroutine
>>> &GUS::Supported::UnflattenBioperlFeatures::preprocess called at
>>> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 63,
>>> <GEN32> line 65.
>>>
>>> STACK TRACE:
>>>  at
>>> /system/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
>>> line 63
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 59
>>>
>>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>>> called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 365
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>> 'HASH(0x2062960)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>>
>>>
>>> STACK TRACE:
>>>  at $GUS_HOME/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm line 67
>>>
>>> GUS::Supported::BioperlFeatMapperSet::preprocessBioperlSeq('GUS::Supported::BioperlFeatMapperSet=HASH(0x207c9c0)',
>>> 'Bio::Seq::RichSeq=HASH(0x28fe2d0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)')
>>> called at
>>> $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
>>> 365
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xfdd9b0)',
>>> 'HASH(0x2062960)') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
>>>         eval {...} called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>> $GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)',
>>> 'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11
>>>
>>> Today I re-ran the LoadTaxon plugin with a new version of the Taxonomy
>>> (*.dmp) file from May 11 2007, apparently it does not make a new load,
>>> but updates the respective Sres tables, anyway such as the first run
>>> the re-run of LoadTaxon provided these warnings:
>>>
>>> Fri May 11 12:42:27 2007        Merging taxons
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '12' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '30' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '37' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '46' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '67' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '76' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '77' not
>>> in database, skipping
>>> Fri May 11 12:42:27 2007        Doing merge and NCBI tax id '79' not
>>> in database, skipping
>>>
>>> What this exactly means ?
>>>
>>> The first time I ran LoadTaxon I got this log:
>>>
>>> tail LoadTaxon.log
>>> Mon May  7 00:07:35 2007        Deleting TaxonNames when redundant
>>> Mon May  7 00:07:39 2007        0 TaxonName entries deleted
>>>
>>> Mon May  7 00:07:42 2007        TIME    6653 sec  (1:50:53)
>>> Mon May  7 00:07:42 2007        RESULT  1
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.TaxonName: 485022
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.Taxon: 359527
>>> Mon May  7 00:07:47 2007        Rows Written    SRes.GeneticCode: 18
>>> Mon May  7 00:07:47 2007        AlgInvocationId 7
>>> Mon May  7 00:07:47 2007        COMMIT  commit on
>>>
>>> The second time:
>>>
>>> tail LoadTaxon_new.log
>>> Fri May 11 13:07:47 2007        Deleting TaxonNames when redundant
>>> Fri May 11 13:07:51 2007        288 TaxonName entries deleted
>>>
>>> Fri May 11 13:07:55 2007        TIME    1528 sec  (0:25:28)
>>> Fri May 11 13:07:55 2007        RESULT  1
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.TaxonName: 4023
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.Taxon: 2263
>>> Fri May 11 13:07:56 2007        Rows Written    SRes.GeneticCode: 0
>>> Fri May 11 13:07:56 2007        AlgInvocationId 56
>>> Fri May 11 13:07:56 2007        COMMIT  commit on
>>>
>>> I just checked the sres.taxonname and it has Leishmania guyanensis
>>> there:
>>>
>>> SELECT
>>> "taxon_name_id","taxon_id","name","unique_name_variant","name_class","modification_date","row_project_id","row_alg_invocation_id"
>>> FROM "sres"."taxonname" WHERE
>>> "name" = 'Leishmania guyanensis';
>>>  taxon_name_id | taxon_id |         name          |
>>> unique_name_variant |   name_class    |     modification_date     |
>>> row_project_id | row_alg_invocation_id
>>> ---------------+----------+-----------------------+---------------------+-----------------+---------------------------+----------------+-----------------------
>>>         369208 |    96595 | Leishmania guyanensis
>>> |                     | scientific name | 2007-05-06 23:41:16.98889
>>> |              1 |                     7
>>> (1 row)
>>>
>>> According to the log, it could be an
>>> UnflattenBioperlFeatures::preprocess error too...
>>>
>>> Some of th GIs (L. guyanensis) I am trying to load with the ISF
>>> pluging are:
>>>
>>> 104530485
>>> 60280340
>>> 110816091
>>> 76577720
>>> 76577719
>>> 76577718
>>>
>>> Thanks for any help you might provide.
>>>
>>> Cheers, Alberto
>>>