chado bulk_load error

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chado bulk_load error

James Lewis
Hi,

I am trying to load a gff3 file into my chado database using the bulk_load script, and this is what I get:

(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...Done.
Preparing data for inserting into the chado_post database
(This may take a while ...)
Dropping cds temp tables...
Creating cds temp tables...
NOTICE:  CREATE TABLE will create implicit sequence "tmp_cds_handler_cds_row_id_seq" for serial column "tmp_cds_handler.cds_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "tmp_cds_handler_pkey" for table "tmp_cds_handler"
NOTICE:  CREATE TABLE will create implicit sequence "tmp_cds_handler_relationship_rel_row_id_seq" for serial column "tmp_cds_handler_relationship.rel_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "tmp_cds_handler_relationship_pkey" for table "tmp_cds_handler_relationship"
Loading data into feature table ...
Loading data into featureloc table ...
Loading data into feature_relationship table ...
Loading data into featureprop table ...
Skipping feature_cvterm table since the load file is empty...
Skipping synonym table since the load file is empty...
Skipping feature_synonym table since the load file is empty...
Loading data into dbxref table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Loading data into cvterm table ...
Skipping db table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping organism table since the load file is empty...
DBD::Pg::db commit failed: ERROR:  insert or update on table "feature_relationship" violates foreign key constraint "feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(6104) is not present in table "feature". at /home/gmod/Documents/Software/tripal/gmod-1.0/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4.
commit failed: ERROR:  insert or update on table "feature_relationship" violates foreign key constraint "feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(6104) is not present in table "feature". at /home/gmod/Documents/Software/tripal/gmod-1.0/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> line 4.

Any ideas what is going wrong here, and what I can do to fix it? I checked the gff3 file and it looks ok to me (but there might be something I missed).

Thanks in advance for any advice offered!

-James

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Re: chado bulk_load error

Scott Cain
Hi James,

Errors like that are usually a result of flawed GFF.  A few suggestions:

* Run the GFF through the GFF3 validator:

  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

though be aware that the Chado loader places additional restrictions
on the format.  See the perldoc for the loader for more information.

* Use the --save_files flag when running it so you can see where in
the GFF file it choked.

* If you can't sort it out, try trimming down your GFF to a managable
size that reproduces the problem and post it to the list.

* Sometimes those types of errors result from conflicts with data that
is already in the database; did you already load some data?

Scott

On Tue, Aug 24, 2010 at 5:02 PM, James Lewis <[hidden email]> wrote:

> Hi,
>
> I am trying to load a gff3 file into my chado database using the bulk_load
> script, and this is what I get:
>
> (Re)creating the uniquename cache in the database...
> Creating table...
> Populating table...
> Creating indexes...Done.
> Preparing data for inserting into the chado_post database
> (This may take a while ...)
> Dropping cds temp tables...
> Creating cds temp tables...
> NOTICE:  CREATE TABLE will create implicit sequence
> "tmp_cds_handler_cds_row_id_seq" for serial column
> "tmp_cds_handler.cds_row_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "tmp_cds_handler_pkey" for table "tmp_cds_handler"
> NOTICE:  CREATE TABLE will create implicit sequence
> "tmp_cds_handler_relationship_rel_row_id_seq" for serial column
> "tmp_cds_handler_relationship.rel_row_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "tmp_cds_handler_relationship_pkey" for table "tmp_cds_handler_relationship"
> Loading data into feature table ...
> Loading data into featureloc table ...
> Loading data into feature_relationship table ...
> Loading data into featureprop table ...
> Skipping feature_cvterm table since the load file is empty...
> Skipping synonym table since the load file is empty...
> Skipping feature_synonym table since the load file is empty...
> Loading data into dbxref table ...
> Loading data into feature_dbxref table ...
> Skipping analysisfeature table since the load file is empty...
> Loading data into cvterm table ...
> Skipping db table since the load file is empty...
> Skipping cv table since the load file is empty...
> Skipping analysis table since the load file is empty...
> Skipping organism table since the load file is empty...
> DBD::Pg::db commit failed: ERROR:  insert or update on table
> "feature_relationship" violates foreign key constraint
> "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(6104) is not present in table "feature". at
> /home/gmod/Documents/Software/tripal/gmod-1.0/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm
> line 2651, <$fh> line 4.
> commit failed: ERROR:  insert or update on table "feature_relationship"
> violates foreign key constraint "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(6104) is not present in table "feature". at
> /home/gmod/Documents/Software/tripal/gmod-1.0/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm
> line 2651, <$fh> line 4.
>
> Any ideas what is going wrong here, and what I can do to fix it? I checked
> the gff3 file and it looks ok to me (but there might be something I missed).
>
> Thanks in advance for any advice offered!
>
> -James
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



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

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