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

Tue Apr 27 09:43:06 EDT 2010

Hi Wangjun,

I'm cc'ing this back to the schema mailing list; please keep the
discussion on the list.

First, to answer you question about your query: the error message told
you that feature_id 517344 is not in the database, so it's not
terribly surprising that when you queried for it, you came up empty
:-)

I'm not exactly sure what is happening, but I'll give you a little
background: when you store a match feature in Chado, it needs two
features to map coordinates to: the "main" one (typically a chromosome
or contig), and the thing you are trying to map (like a cDNA or EST).
If the cDNA or EST feature is not already in the database, the loader
will do it's best to create a "dummy" feature to take it's place.
This is frequently not ideal; for one thing, it makes the information
that Apollo shows curators less useful.  It is possible to create
those features in the database before loading the match features by
making use of the gmod_fasta2gff3.pl script that comes with Chado.

Now, to what might be happening in your particular case: the
feature_id that is being referred to is quite a bit less than new IDs
that are being generated for your current load, and the missing
feature_id is for one of these auto-created dummy features, presumably
from a previously attempted load.  If that feature didn't get created
(and it appears that it did not, since it's not in the feature table),
then a table that the gff loader uses as a cache may be corrupted.
Try rerunning the loader with the --recreate_cache option.

Scott

2010/4/27 wangjun19820303 <wangjun19820303 at 163.com>:
> 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
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Gmod-devel mailing list
>> Gmod-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>
>
>
> --
> ===> PLEASE KEEP RESPONSES ON THE LIST <===
> http://gmod.org/wiki/GMOD_Logo_Program
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> ________________________________
> 网易免费域名邮箱正式上线

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research