Re: [GMOD-devel] Load the GFF3

[Scott C. <sc...@sc...>]

Hello Inna,

Two things to try:

1. Check that there really is a line with "ID=match_1" before the
first line with "Parent=match_1"

2. Try the load again with --recreate_cache added the the first load
command.  Any time you get a failed load, you should add the
--recreate_cache to the next bulk load command as the untimely death
of the loader leaves a temporary table in the database in a corrupted
state.

As an aside, I'm glad to see loading from stdin works--I haven't tried
it in years.

Scott


On Fri, May 22, 2009 at 10:41 AM, Rytsareva, Inna (I)
<IRy...@do...> wrote:
> Hello.
>
> I have a GFF3 file for maize. It's 200 MB. When I try to load it into
> Postgres Database an error occurs:
>
> /bin/sh: line 1:  6492 Done                    cat maize_whole.gff3
>       6493 Killed                  | /usr/bin/gmod_bulk_load_gff3.pl
> --dbuser postgres --dbhost localhost --dbname chado-maize_whole --analysis
> --organism maize_whole
>
> make: *** [maize_whole.create] Error 137
>
> I tried to split this file into 10 files (for each chromosome) and load.
> First one was loaded successfully, but when I'm tring to load others an
> error occurs:
>
> [n006514@eluxb08 ~/workspace]$ cat maize_whole_7.gff3 |
> /usr/bin/gmod_bulk_load_gff3.pl --dbuser postgres --dbhost localhost
> --dbname chado-maize_whole --analysis --organism maize_whole
>
> Preparing data for inserting into the chado-maize_whole database
> (This may take a while ...)
>
> no parent match_1;
> you probably need to rerun the loader with the --recreate_cache option
>
> Issuing rollback() for database handle being DESTROY'd without explicit
> disconnect(), <STDIN> line 1215.
>
> Please, response.
>
> Inna Rytsareva
> Discovery Information Management
> Dow AgroSciences
> Indianapolis, IN
> 317-337-4716
>
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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