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From: <hen...@gm...> - 2005-08-12 19:41:20
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Hello everyone,
My name is Henrique and I'll be helping Thiago out with our GUS
implementation around here. Well, we're trying to implement GBParser
plugin, and we achieved some level of success, managing to populate
our databases with nucleotides recently downloaded from Genbank.
However, we're having some problem with protein archives, in Genbank
format. Seems that NCBI made some minor (I couldn't find any major
changes other than its name - GenPept -, and its extension, now .gp)
changes to its format, and I've got the following error while trying
to populate GUS:
$ ga GUS::Community::Plugin::GBParser --file
/home/juca/Tryp_rangeli.gp --db_rel_id 22 --gbRel '148.0' --commit
Fri Aug 12 16:41:35 2005 ARGS algoinvo 1
Fri Aug 12 16:41:35 2005 ARGS comment
Fri Aug 12 16:41:35 2005 ARGS commit 1
Fri Aug 12 16:41:35 2005 ARGS db_rel_id 22
Fri Aug 12 16:41:35 2005 ARGS debug
Fri Aug 12 16:41:35 2005 ARGS div
Fri Aug 12 16:41:35 2005 ARGS failTolerance 100
Fri Aug 12 16:41:35 2005 ARGS file /home/juca/Tryp_rangeli.gp
Fri Aug 12 16:41:35 2005 ARGS gbRel 148.0
Fri Aug 12 16:41:35 2005 ARGS group
Fri Aug 12 16:41:35 2005 ARGS gusconfigfile =20
/usr/local/GUS/gus.properties
Fri Aug 12 16:41:35 2005 ARGS project
Fri Aug 12 16:41:35 2005 ARGS sqlVerbose
Fri Aug 12 16:41:35 2005 ARGS start
Fri Aug 12 16:41:35 2005 ARGS testnumber
Fri Aug 12 16:41:35 2005 ARGS updateAll
Fri Aug 12 16:41:35 2005 ARGS usage
Fri Aug 12 16:41:35 2005 ARGS user
Fri Aug 12 16:41:35 2005 ARGS verbose
Fri Aug 12 16:41:35 2005 ARGS veryVerbose
Fri Aug 12 16:41:35 2005 COMMIT commit on
Fri Aug 12 16:41:35 2005 ALGINVID 21
Fri Aug 12 16:41:35 2005 COMMIT commit on
Maximum number of objects set to 50000
Fri Aug 12 16:41:35 2005 RELEASE 148.0
=20
Fri Aug 12 16:41:35 2005 FILE /home/juca/Tryp_rangeli.gp
=20
VLD CBIL::Bio::GenBank::Locus 1
VLD CBIL::Bio::GenBank::Definition 1
VLD CBIL::Bio::GenBank::Accession 1
VLD CBIL::Bio::GenBank::Version 1
ERR LINE=3D5 unrequireable class Dbsource
ERROR:
Can't locate CBIL/Bio/GenBank/Dbsource.pm in @INC (@INC contains:
/usr/local/GUS/gus_home/lib/perl
/usr/local/GUS/gus_home/lib/perl/5.8.6/i386-linux-thread-multi
/usr/local/GUS/gus_home/lib/perl/5.8.6
/usr/local/GUS/gus_home/lib/perl/i386-linux-thread-multi
/usr/local/GUS/gus_home/lib/perl/5.8.5
/usr/local/GUS/gus_home/lib/perl/5.8.4
/usr/local/GUS/gus_home/lib/perl/5.8.3
/usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
/usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3
/usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
/usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3
/usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.6/i386-linux-thread-multi /usr/lib/perl5/5.8.6 .)
at (eval 29) line 3, <GEN0> line 87.
=20
STACK TRACE:
at (eval 29) line 3
eval 'require CBIL::Bio::GenBank::Dbsource
;' called at /usr/local/GUS/gus_home/lib/perl/CBIL/Bio/GenBank/Entry.pm lin=
e 39
CBIL::Bio::GenBank::Entry::parse('CBIL::Bio::GenBank::Entry=3DHASH(=
0x9f9fcf4)',
'CBIL::Bio::GenBank::ArrayStream=3DHASH(0x9f9fc88)') called at
/usr/local/GUS/gus_home/lib/perl/CBIL/Bio/GenBank/BaseObject.pm line
13
CBIL::Bio::GenBank::BaseObject::new('CBIL::Bio::GenBank::Entry',
'HASH(0x9f9fcac)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
203
GUS::Community::Plugin::GBParser::processEntry('GUS::Community::Plu=
gin::GBParser=3DHASH(0x91dc570)',
'CBIL::Bio::GenBank::ArrayStream=3DHASH(0x9f9fc88)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
185
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
184
GUS::Community::Plugin::GBParser::run('GUS::Community::Plugin::GBPa=
rser=3DHASH(0x91dc570)',
'HASH(0x9f22cf8)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'ARRAY(0x91a1560)') called at /usr/local/GUS/gus_home/bin/ga line 11
=20
=20
ERR LINE=3D6 unparsed line class: standard.
=20
ERR LINE=3D7 unparsed line created: Nov 1, 1997.
=20
ERR LINE=3D8 unparsed line sequence updated: Nov 1, 1997=
.
=20
ERR LINE=3D9 unparsed line annotation updated: Sep 13, 2=
005.
=20
ERR LINE=3D10 unparsed line xrefs: Z54192.1, CAA90897.1
=20
ERR LINE=3D11 unparsed line xrefs (non-sequence
databases): HSSPQ27709, InterProIPR003299,
=20
ERR LINE=3D12 unparsed line InterProIPR011992,
InterProIPR002048, PfamPF00036, PRINTSPR01362,
=20
ERR LINE=3D13 unparsed line ProDomPD000012,
SMARTSM00054, PROSITEPS00018, PROSITEPS50222
=20
VLD CBIL::Bio::GenBank::Keywords 1
VLD CBIL::Bio::GenBank::Source 1
VLD CBIL::Bio::GenBank::Reference 1
VLD CBIL::Bio::GenBank::Comment 1
RUN 1..204
RUN 1..204
RUN 1..204
RUN 39..74
RUN 52..63
RUN 75..110
RUN 120..155
RUN 133..144
RUN 157..192
RUN 170..181
VLD CBIL::Bio::GenBank::Features 1
VLD CBIL::Bio::GenBank::Origin 1
Fri Aug 12 16:41:35 2005 STATUS N=3D1 ACC=3DQ27052 TOTAL_OBJECTS=
=3D16
=20
ERROR:
Can't open failure file gbparserFailures/1.gb at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
1289, <GEN0> line 87.
=20
STACK TRACE:
at /usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line =
1289
GUS::Community::Plugin::GBParser::handleFailure('GUS::Community::Pl=
ugin::GBParser=3DHASH(0x91dc570)',
'ARRAY(0x9d3d034)', 'CBIL::Util::A=3DHASH(0x9dbbc4c)',
'\x{a}ERROR:\x{a}Can\'t call method "new" on an undefined value at
/us...') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
187
GUS::Community::Plugin::GBParser::run('GUS::Community::Plugin::GBPa=
rser=3DHASH(0x91dc570)',
'HASH(0x9f22cf8)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'ARRAY(0x91a1560)') called at /usr/local/GUS/gus_home/bin/ga line 11
Could I be missing something? I'm pretty much unfamiliar with GUS and
I trying to get the hang of it ;)
Thanks in advance!
--=20
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
"As soon as you concern yourself with the "good" and "bad" of your fellows,=
=20
you create an opening in your heart for maliciousness to enter. Testing,=20
competing with, and criticizing others weaken and defeat you."
Morihei Ueshiba, O-Sensei (1883-1969)
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