Re: [Gusdev-gusdev] LoadNRDB error

[Poliana M. <pol...@gm...>]

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
> >
> >
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