From: <hen...@gm...> - 2005-11-03 15:26:53
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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) |