Re: [Gusdev-gusdev] LoadNRDB error

[Deborah P. <pi...@pc...>]

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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