gff to chado error

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gff 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:




Thanks,
Karthik

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Re: gff to chado error

Becksfort, Jared
That constraint refers to the start and stop point of the feature location record.  The fmin must be less than or equal to the fmax.  Probably 9527 and 9193 (or 2827675 and 196521) should be swapped in your input file that is used to generate loading file.

-----Original Message-----
From: Karthik [mailto:[hidden email]]
Sent: Friday, July 02, 2010 12:19 PM
To: [hidden email]
Subject: [Gmod-schema] gff to chado error. .


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:




Thanks,
Karthik

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Re: gff to chado error

Scott Cain
Quite right, the first three integers are ids: featureloc_id,
feature_id and srcfeature_id, and the next two are fmin and fmax.
Looking exactly for those values though won't work, because GFF uses
base coordinates and Chado uses interbase coordinates, so you need to
look for a start of 9528 and end of 9193.

Scott

On Fri, Jul 2, 2010 at 2:00 PM, Becksfort, Jared
<[hidden email]> wrote:

> That constraint refers to the start and stop point of the feature location record.  The fmin must be less than or equal to the fmax.  Probably 9527 and 9193 (or 2827675 and 196521) should be swapped in your input file that is used to generate loading file.
>
> -----Original Message-----
> From: Karthik [mailto:[hidden email]]
> Sent: Friday, July 02, 2010 12:19 PM
> To: [hidden email]
> Subject: [Gmod-schema] gff to chado error. .
>
>
> 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:
>
>
>
>
> Thanks,
> Karthik
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/gff-to-chado-error-tp512721p512721.html
> Sent from the gmod-schema mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
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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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Re: gff to chado error

Karthik Narayan Muthuraman
Thank you. I'll try swapping the coordinates.

Regards,
Karthik

On Fri, Jul 2, 2010 at 2:04 PM, Scott Cain <[hidden email]> wrote:
Quite right, the first three integers are ids: featureloc_id,
feature_id and srcfeature_id, and the next two are fmin and fmax.
Looking exactly for those values though won't work, because GFF uses
base coordinates and Chado uses interbase coordinates, so you need to
look for a start of 9528 and end of 9193.

Scott

On Fri, Jul 2, 2010 at 2:00 PM, Becksfort, Jared
<[hidden email]> wrote:
> That constraint refers to the start and stop point of the feature location record.  The fmin must be less than or equal to the fmax.  Probably 9527 and 9193 (or 2827675 and 196521) should be swapped in your input file that is used to generate loading file.
>
> -----Original Message-----
> From: Karthik [mailto:[hidden email]]
> Sent: Friday, July 02, 2010 12:19 PM
> To: [hidden email]
> Subject: [Gmod-schema] gff to chado error. .
>
>
> 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:
>
>
>
>
> Thanks,
> Karthik
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/gff-to-chado-error-tp512721p512721.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?
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> https://lists.sourceforge.net/lists/listinfo/gmod-schema
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>
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>
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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



--
Regards,
Karthik Narayan

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