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Re: [GUSDEV] LoadNRDB error
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From: Michael S. <msa...@pc...> - 2005-11-03 15:32:23
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Hi Henrique,
It looks like your connection string (from your command line) is =20
incorrect. Try:
dbi:Pg:dbname=3Dgustest
--Mike
On Nov 3, 2005, at 10:26 AM, Henrique Juc=E1 wrote:
> Hi all,
>
> I am trying to load nr to GUS, without success.... here's my command
> line and the error output:
>
> [juca1@kineto3 perl]$ ga GUS::Supported::Plugin::LoadNRDB
> --externalDatabaseName 'GenBank' --externalDatabaseVersion 'unknown'
> --gitax /gus/GUS-Files/gi_taxid_prot.dmp --nrdbFile /gus/GUS-Files/nr
> --sourceDB '2:gb, 3:emb, 4:dbj, 5:pir, 6:prf, 7:sp, 8:pdb, 9:pat,
> 10:bbs, 11:gnl, ref:168, 12:genpept' --tempLogin 'xxxx' --tempPassword
> 'xxxxxx' --dbiStr 'dbi:Pg:host=3Dlocalhost.localdomain;sid=3Dgustest'
> --verbose --maketemp
>
> Thu Nov 3 13:18:51 2005 ARG algoinvo 1
> Thu Nov 3 13:18:51 2005 ARG comment
> Thu Nov 3 13:18:51 2005 ARG commit 0
> Thu Nov 3 13:18:51 2005 ARG dbiStr
> dbi:Pg:host=3Dlocalhost.localdomain;sid=3Dgustest
> Thu Nov 3 13:18:51 2005 ARG debug 0
> Thu Nov 3 13:18:51 2005 ARG delete 0
> Thu Nov 3 13:18:51 2005 ARG externalDatabaseName =20
> GenBank
> Thu Nov 3 13:18:51 2005 ARG externalDatabaseVersion =20
> unknown
> Thu Nov 3 13:18:51 2005 ARG gitax
> /gus/GUS-Files/gi_taxid_prot.dmpThu Nov 3 13:18:51 2005 ARG
> group
> Thu Nov 3 13:18:51 2005 ARG gusconfigfile /gus/GUS/=20
> gus.properties
> Thu Nov 3 13:18:51 2005 ARG help
> Thu Nov 3 13:18:51 2005 ARG helpHTML
> Thu Nov 3 13:18:51 2005 ARG makeTemp 1
> Thu Nov 3 13:18:51 2005 ARG nrdbFile /gus/GUS-=20
> Files/nr
> Thu Nov 3 13:18:51 2005 ARG plugin 0
> Thu Nov 3 13:18:51 2005 ARG project
> Thu Nov 3 13:18:51 2005 ARG restart
> Thu Nov 3 13:18:51 2005 ARG restartTempTable 0
> Thu Nov 3 13:18:51 2005 ARG sourceDB 2:gb, 3:emb,
> 4:dbj, 5:pir, 6:prf, 7:sp, 8:pdb, 9:pat, 10:bbs, 11:gnl, ref:168,
> 12:genpept
> Thu Nov 3 13:18:51 2005 ARG sqlVerbose 0
> Thu Nov 3 13:18:51 2005 ARG tempLogin juca
> Thu Nov 3 13:18:51 2005 ARG tempPassword saci10
> Thu Nov 3 13:18:51 2005 ARG testnumber1
> Thu Nov 3 13:18:51 2005 ARG testnumber2
> Thu Nov 3 13:18:51 2005 ARG user
> Thu Nov 3 13:18:51 2005 ARG verbose 1
> Thu Nov 3 13:18:51 2005 ARG veryVerbose 0
> Thu Nov 3 13:18:51 2005 AlgInvocationId 59
> Thu Nov 3 13:18:51 2005 COMMIT commit off
> Thu Nov 3 13:18:51 2005 There are 12 entries in the source
> database hashThu Nov 3 13:20:11 2005 There are 7251218 gi to
> taxon_id pairs
>
> DBI connect('host=3Dlocalhost.localdomain;sid=3Dgustest','juca',...)
> failed: invalid connection option "sid"
> at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadNRDB.pm =20
> line 320
>
> ERROR:
> Can't call method "do" on an undefined value at
> /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadNRDB.pm line 323.
>
> STACK TRACE:
> at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadNRDB.pm =20
> line 323
> GUS::Supported::Plugin::LoadNRDB::makeTempTable=20
> ('GUS::Supported::Plugin::LoadNRDB=3DHASH(0x99a1504)','HASH=20
> (0x9f517fc)','HASH(0x9a39270)')
> called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadNRDB.pm
> line 210
> GUS::Supported::Plugin::LoadNRDB::run=20
> ('GUS::Supported::Plugin::LoadNRDB=3DHASH(0x99a1504)','HASH(0xa13d12c)')=
> called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 520
> eval {...} called at
> /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 512
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20
> ('GUS::PluginMgr::GusApplication=3DHASH=20
> (0x9980c18)','GUS::Supported::Plugin::LoadNRDB',1)
> called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 430
> GUS::PluginMgr::GusApplication::doMajorMode_Run=20
> ('GUS::PluginMgr::GusApplication=3DHASH=20
> (0x9980c18)','GUS::Supported::Plugin::LoadNRDB')
> called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 337
> GUS::PluginMgr::GusApplication::doMajorMode=20
> ('GUS::PluginMgr::GusApplication=3DHASH=20
> (0x9980c18)','GUS::Supported::Plugin::LoadNRDB')
> called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 246
> GUS::PluginMgr::GusApplication::parseAndRun=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x9980c18)','ARRAY(0x99946a8)')
> called at /gus/GUS/gus_home/bin/ga line 11
>
> That option 'sid' is listed on the help file, so why is that the =20
> error?
>
> Thanks for the attention,
>
>
>
> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
> "As soon as you concern yourself with the "good" and "bad" of your =20
> fellows,
> you create an opening in your heart for maliciousness to enter. =20
> Testing,
> competing with, and criticizing others weaken and defeat you."
>
> Morihei Ueshiba, O-Sensei (1883-1969)
>
>
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