gff3 to chado error

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gff3 to chado error

Karthik-7

Hello, I'm trying to load gff3 data to chado using gmod_bulk_load_gff3.pl.
Since it was a huge file, I split the file into smaller chunks based on
source after sorting. When I try to load the smaller files, it fails in the
constraint "featureloc_c2".

Are there changes I have to make in my data ? The same gff file was loaded
in Mysql and works fine gbrowse. Below is the error I get.



Loading data into feature table ...
Loading data into featureloc table ...
DBD::Pg::db pg_endcopy failed: ERROR:  new row for relation "featureloc"
violates check constraint "featureloc_c2"
CONTEXT:  COPY featureloc, line 86154: "87625   282675  196521  9527    9193  
1       \N      0       0" at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 2739, <$fh> line
1217773.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: calling endcopy for featureloc failed:


Also, I searched my gff3 file for '\t9526\t' and did not find any
occurrence. The same problem occurs for all the split files.



Thanks,
Karthik
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Re: gff3 to chado error

Scott Cain
Hi Karthik,

The constraint on featureloc that is being violated is that fmin must
be less than or equal to fmax, which is also required by the GFF3
spec.  Some adaptors for GBrowse (certainly Bio::DB::GFF, and possibly
Bio::DB::SeqFeature::Store) are more relaxed on this requirement.

Scott


On Fri, Jul 2, 2010 at 1:43 PM, Karthik <[hidden email]> wrote:

>
> Hello, I'm trying to load gff3 data to chado using gmod_bulk_load_gff3.pl.
> Since it was a huge file, I split the file into smaller chunks based on
> source after sorting. When I try to load the smaller files, it fails in the
> constraint "featureloc_c2".
>
> Are there changes I have to make in my data ? The same gff file was loaded
> in Mysql and works fine gbrowse. Below is the error I get.
>
>
>
> Loading data into feature table ...
> Loading data into featureloc table ...
> DBD::Pg::db pg_endcopy failed: ERROR:  new row for relation "featureloc"
> violates check constraint "featureloc_c2"
> CONTEXT:  COPY featureloc, line 86154: "87625   282675  196521  9527    9193
> 1       \N      0       0" at
> /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 2739, <$fh> line
> 1217773.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: calling endcopy for featureloc failed:
>
>
> Also, I searched my gff3 file for '\t9526\t' and did not find any
> occurrence. The same problem occurs for all the split files.
>
>
>
> Thanks,
> Karthik
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/gff3-to-chado-error-tp512726p512726.html
> Sent from the gmod-schema mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
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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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