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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)
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From: Poliana M. <pol...@gm...> - 2005-02-23 13:49:39
|
I am trying to run the LoadNRD, but I have the following error:
[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
--plugin --delete --commit
Wed Feb 23 09:25:04 2005 ***COMMIT ON***
There are 12 entries in the source database hash
Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
Wed Feb 23 10:30:27 2005 1000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:31:20 2005 2000 sets have been processed
and put in the NRDBTemp table
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 6374.
Wed Feb 23 10:31:47 2005 3000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:32:10 2005 4000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:33:15 2005 6000 sets have been processed
and put in the NRDBTemp table
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 19995.
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 20179.
Wed Feb 23 10:34:03 2005 8000 sets have been processed
and put in the NRDBTemp table
......
--------------------------------------------------------------------------------------------------------------
somebody has idea of as to correct?
Poliana
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|
From: Deborah P. <pi...@pc...> - 2005-02-23 15:38:04
|
I believe you are missing a couple ext_db_rel_ids for the source
databases in the nr file. This is the string I use. Of course the
release_ids are specific to our database.
7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd
also, extDbRelId is an int, not a string
Debbie
Poliana Mateus wrote:
>I am trying to run the LoadNRD, but I have the following error:
>
>[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
>--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
>--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
>--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
>--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
>--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
>--plugin --delete --commit
>
>Wed Feb 23 09:25:04 2005 ***COMMIT ON***
>
>There are 12 entries in the source database hash
>Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
>
>Wed Feb 23 10:30:27 2005 1000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:31:20 2005 2000 sets have been processed
> and put in the NRDBTemp table
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 6374.
>
>Wed Feb 23 10:31:47 2005 3000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:32:10 2005 4000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:33:15 2005 6000 sets have been processed
> and put in the NRDBTemp table
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 19995.
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 20179.
>Wed Feb 23 10:34:03 2005 8000 sets have been processed
> and put in the NRDBTemp table
>
>......
>
>--------------------------------------------------------------------------------------------------------------
>
>somebody has idea of as to correct?
>
>Poliana
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Poliana M. <pol...@gm...> - 2005-02-24 11:08:23
|
Hi Debbie
Yesterday I started to load the LoadNRDB and still no finished. This normal?
It sees output:
Wed Feb 23 13:17:46 2005 ***COMMIT ON***
There are 15 entries in the source database hash
Wed Feb 23 14:06:52 2005 There are 5821294 gi to taxon_id pairs
Wed Feb 23 14:11:53 2005 1000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:12:16 2005 2000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:12:40 2005 3000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:13:07 2005 4000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:13:51 2005 6000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:14:37 2005 8000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:15:23 2005 10000 sets have been processed
and put in the NRDBTemp table
........
Poliana
On Wed, 23 Feb 2005 10:42:31 -0500, Deborah Pinney
<pi...@pc...> wrote:
> I believe you are missing a couple ext_db_rel_ids for the source
> databases in the nr file. This is the string I use. Of course the
> release_ids are specific to our database.
>
> 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd
>
> also, extDbRelId is an int, not a string
>
> Debbie
>
>
> Poliana Mateus wrote:
>
> >I am trying to run the LoadNRD, but I have the following error:
> >
> >[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
> >--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
> >--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
> >--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
> >--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
> >--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
> >--plugin --delete --commit
> >
> >Wed Feb 23 09:25:04 2005 ***COMMIT ON***
> >
> >There are 12 entries in the source database hash
> >Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
> >
> >Wed Feb 23 10:30:27 2005 1000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:31:20 2005 2000 sets have been processed
> > and put in the NRDBTemp table
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 6374.
> >
> >Wed Feb 23 10:31:47 2005 3000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:32:10 2005 4000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:33:15 2005 6000 sets have been processed
> > and put in the NRDBTemp table
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 19995.
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 20179.
> >Wed Feb 23 10:34:03 2005 8000 sets have been processed
> > and put in the NRDBTemp table
> >
> >......
> >
> >--------------------------------------------------------------------------------------------------------------
> >
> >somebody has idea of as to correct?
> >
> >Poliana
> >
> >
> >-------------------------------------------------------
> >SF email is sponsored by - The IT Product Guide
> >Read honest & candid reviews on hundreds of IT Products from real users.
> >Discover which products truly live up to the hype. Start reading now.
> >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>
|
|
From: Poliana M. <pol...@gm...> - 2005-02-24 15:43:08
|
Thanks... When that to finish I sending the result! Poliana On Thu, 24 Feb 2005 10:23:03 -0500, John Iodice <io...@pc...> wrote: > Poliana, > > I ran LoadNRDB a couple of weeks ago, and it did take about a day to > load all of NRDB. So don't worry about that. Do check out the final > output when it finishes; if you see anything amiss there, post to the > group or email me or Debbie. > > John > > On Thu, 2005-02-24 at 06:08, Poliana Mateus wrote: > > Hi Debbie > > > > Yesterday I started to load the LoadNRDB and still no finished. This normal? > > > > It sees output: > > > > Wed Feb 23 13:17:46 2005 ***COMMIT ON*** > > > > There are 15 entries in the source database hash > > Wed Feb 23 14:06:52 2005 There are 5821294 gi to taxon_id pairs > > > > Wed Feb 23 14:11:53 2005 1000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:12:16 2005 2000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:12:40 2005 3000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:13:07 2005 4000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:13:51 2005 6000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:14:37 2005 8000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:15:23 2005 10000 sets have been processed > > and put in the NRDBTemp table > > > > > > ........ > > > > Poliana > > > > > > On Wed, 23 Feb 2005 10:42:31 -0500, Deborah Pinney > > <pi...@pc...> wrote: > > > I believe you are missing a couple ext_db_rel_ids for the source > > > databases in the nr file. This is the string I use. Of course the > > > release_ids are specific to our database. > > > > > > 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd > > > > > > also, extDbRelId is an int, not a string > > > > > > Debbie > > > > > > > > > Poliana Mateus wrote: > > > > > > >I am trying to run the LoadNRD, but I have the following error: > > > > > > > >[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB > > > >--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus" > > > >--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl" > > > >--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps" > > > >--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp" > > > >--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp > > > >--plugin --delete --commit > > > > > > > >Wed Feb 23 09:25:04 2005 ***COMMIT ON*** > > > > > > > >There are 12 entries in the source database hash > > > >Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs > > > > > > > >Wed Feb 23 10:30:27 2005 1000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:31:20 2005 2000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 6374. > > > > > > > >Wed Feb 23 10:31:47 2005 3000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:32:10 2005 4000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:33:15 2005 6000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 19995. > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 20179. > > > >Wed Feb 23 10:34:03 2005 8000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >...... > > > > > > > >-------------------------------------------------------------------------------------------------------------- > > > > > > > >somebody has idea of as to correct? > > > > > > > >Poliana > > > > > > > > > > > >------------------------------------------------------- > > > >SF email is sponsored by - The IT Product Guide > > > >Read honest & candid reviews on hundreds of IT Products from real users. > > > >Discover which products truly live up to the hype. Start reading now. > > > >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > > > >_______________________________________________ > > > >Gusdev-gusdev mailing list > > > >Gus...@li... > > > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > SF email is sponsored by - The IT Product Guide > > Read honest & candid reviews on hundreds of IT Products from real users. > > Discover which products truly live up to the hype. Start reading now. > > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- > John Iodice > Bioinformatics Software Engineer > Computational Biology and Informatics Lab > University of Pennsylvania > http://cbil.upenn.edu > > |
|
From: Michael S. <msa...@pc...> - 2005-11-03 15:32:23
|
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)
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. =20=
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: <hen...@gm...> - 2005-11-03 16:33:59
|
Thanks Michael, it worked. But shouldn't this lines from the --help be
updated then?
The help file from LoadNRDB prints:
--dbiStr *string*
server and machine for temp table, e.g.
dbi:Oracle:host=3Derebus.pcbi.upenn.edu;sid=3Dgusdev
Shouldn't that line be corrected?
Another thing, I've been trying to update sres.externaldatabase table
with no success.
$ ga GUS::Supported::Plugin::InsertExternalDatabase --name tpg --commit
Thu Nov 3 14:07:35 2005 ARG algoinvo 1
Thu Nov 3 14:07:35 2005 ARG comment
Thu Nov 3 14:07:35 2005 ARG commit 1
Thu Nov 3 14:07:35 2005 ARG debug 0
Thu Nov 3 14:07:35 2005 ARG group
Thu Nov 3 14:07:35 2005 ARG gusconfigfile /gus/GUS/gus.proper=
ties
Thu Nov 3 14:07:35 2005 ARG help
Thu Nov 3 14:07:35 2005 ARG helpHTML
Thu Nov 3 14:07:35 2005 ARG name tpg
Thu Nov 3 14:07:35 2005 ARG project
Thu Nov 3 14:07:35 2005 ARG sqlVerbose 0
Thu Nov 3 14:07:35 2005 ARG user
Thu Nov 3 14:07:35 2005 ARG verbose 0
Thu Nov 3 14:07:35 2005 ARG veryVerbose 0
Thu Nov 3 14:07:35 2005 AlgInvocationId 63
Thu Nov 3 14:07:35 2005 COMMIT commit on
DBD::Pg::st execute failed: ERROR: duplicate key violates unique
constraint "pk_externaldatabase"
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.ExternalDatabase ( group_write, other_read,
group_read, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
Values: 1, 1, 1, tpg, 1, 1, 21, 0, 63, 1, 1, 1 at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
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(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',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(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11
STACK TRACE:
at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a} INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
INSERT INTO SRes.ExternalDatabase ( group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
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(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',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(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11
I uploaded to this table a ExternalDatabases.xml archive, using
LoadGusXml. From what I could understand from that error, seems that
id was supplied to another entry (and indeed it was). I guess what is
happening is some kind of conflict between the entries I uploaded in
this tables and the new entries I'm trying to submit. I looked for any
conflicts among the entries I need to create (nr, tpe, tpd, tpg and a
few others) and the contents of the xml file, and I couldn't find any
duplicate entries.
Thanks again for the quick replies,
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)
|
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