[GUSDEV] LoadNRDB error

[<hen...@gm...>]

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=20
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    GenBank
Thu Nov  3 13:18:51 2005        ARG     externalDatabaseVersion unknown
Thu Nov  3 13:18:51 2005        ARG     gitax =20
/gus/GUS-Files/gi_taxid_prot.dmpThu Nov  3 13:18:51 2005        ARG  =20
 group
Thu Nov  3 13:18:51 2005        ARG     gusconfigfile   /gus/GUS/gus.proper=
ties
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-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 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 line 323
        GUS::Supported::Plugin::LoadNRDB::makeTempTable('GUS::Supported::Pl=
ugin::LoadNRDB=3DHASH(0x99a1504)','HASH(0x9f517fc)','HASH(0x9a39270)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadNRDB.pm
line 210
        GUS::Supported::Plugin::LoadNRDB::run('GUS::Supported::Plugin::Load=
NRDB=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('GUS::Plugi=
nMgr::GusApplication=3DHASH(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('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9980c18)','GUS::Supported::Plugin::LoadNRDB')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x9980c18)','GUS::Supported::Plugin::LoadNRDB')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=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 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 fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)