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Re: [Gusdev-gusdev] LoadNRDB error
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From: Poliana M. <pol...@gm...> - 2005-02-24 15:43:08
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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 > > |
