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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 11, Issue 4
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From: <mro...@cs...> - 2007-05-16 23:49:55
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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 > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gusdev-gusdev digest..." > > > 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 >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> 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. >> http://sourceforge.net/powerbar/db2/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------ > > 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 >> > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------- > 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. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest, Vol 11, Issue 4 > ******************************************** > |
