[Gmod-help] Re:Re: [GMOD-devel] help

[wangjun19820303]

hi Dave,
    I　met the same error as the last time .It said 
"DBD::Pg::db commit failed: ERROR:  insert or update on table "featureloc" violates foreign key constraint "featureloc_srcfeature_id_fkey"
DETAIL:  Key (srcfeature_id)=(517344) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4878.
commit failed: ERROR:  insert or update on table "featureloc" violates foreign key constraint "featureloc_srcfeature_id_fkey"
DETAIL:  Key (srcfeature_id)=(517344) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4878.
"

I used the --save option and got the tmp files .But when I run the query :
  select  *  from feature where feature_id = 517344 .It is empty. So why didn't  loader  loaded feature into my database?
Is my gff  file problem?

 Thank you very much!!!

Wangjun


在2010-04-22 02:31:44，"Dave Clements, GMOD Help Desk" <help at gmod.org> 写道：
Hi Wangjun,


I'm CC'ing the Schema/Chado list, which is probably a better place to discuss this question.


I talked to Scott Cain about this:  Make sure that BioPerl and schema are up to date, and if that doesn't fix it, run the loader with the --save option so the tmp files get saved. Then you can find the line in the featureloc file that is offending.  If that approach doesn't result in solving the problem, then we might need to see the GFF that is causing the problem.


Thanks


Dave C


2010/4/15 wangjun19820303 <wangjun19820303 at 163.com>
hi all,
    When I was importing blast result gff3 file into chado database using  gmod_bulk_load_gff3.pl, I got  the errors like this:
    DBD::Pg::db commit failed: ERROR:  insert or update on table "featureloc" violates foreign key constraint "featureloc_srcfeature_id_fkey"
DETAIL:  Key (srcfeature_id)=(177) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4190.
commit failed: ERROR:  insert or update on table "featureloc" violates foreign key constraint "featureloc_srcfeature_id_fkey"
DETAIL:  Key (srcfeature_id)=(177) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4190.
I don't know why and how to handle. Could you help me?
I am looking forward to your reply.

Wangjun




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