Re: [Gmod-schema] gff chado loading question

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Hi Victor:
I encountered similar situations when i did wormbase migration. here is the
wiki page that might help:
http://www.gmod.org/wiki/index.php/Zheng%27s_notes_on_wormbase_migration
especially the section "my experience with chromosome I".

cheers,
Zheng

On Mon, Apr 28, 2008 at 1:56 PM, Scott Cain <cai...@gm...> wrote:

> Hello Victor,
>
> I will have to look into the warnings about the 'my' variable, but I
> don't think that is the main problem.  There is at least on problem with
> the GFF file you pointed to, and I wouldn't be surprised to find more.
> The first problem I found is that it lacks a reference sequence line (at
> least, a proper one).  The first GFF line is this:
>
> NC_007404.1     RefSeq  source  1       2909809 .       +       .
> organism=Thiobacillus%20denitrificans%20ATCC%2025259;mol_type=genomic%20DNA;strain=ATCC%2025259;db_xref=ATCC:25259;db_xref=taxon:292415
>
> It does not have "ID=NC_007404.1".  Also many of the gene models lack
> ID/Parent tags to indicate what belongs to what, which will result in
> fairly difficult to use data (GBrowse certainly won't work correctly).
>
> Scott
>
>
> On Fri, 2008-04-18 at 17:20 +0200, Victor de Jager wrote:
> > Hi all,
> >
> > I have installed a copy of the chado scheme on my local Debian
> > installation following the instructions for Ubuntu.
> > (loaded ontologies 1,2,3 and 4)
> > However but I have a problem with loading a refseq gff file from ncbi.
> > I try to follow the Load gff into Chado page.
> >
> > I want to load
> >
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Thiobacillus_denitrificans_ATCC_25259/NC_007404.gff
> >
> > I created an organism using the select statement on the wiki
> > INSERT INTO organism (abbreviation, genus, species, common_name)
> >                 VALUES ('NC_007404.1', 'Thiobacillus',
> > 'denitrificans', 'Thiobacillus denitrificans ATCC 25259');
> >
> >
> > gmod_gff3_preprocessor.pl --gfffile /tmp/NC_007404.gff --outfile
> > tbd.sorted.gff results in the following error message:
> > --------------
> > "my" variable %seen masks earlier declaration in same scope
> > at /usr/local/share/perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 4199.
> > "my" variable %seen masks earlier declaration in same scope
> > at /usr/local/share/perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 4223.
> > Sorting the contents of /tmp/tmp.gff ...
> >
> > Writing sorted contents to /tmp/tmp.gff.sorted ...
> > ------------
> > tbd.sorted.gff is not created
> >
> > when I try to load the gff as is:
> >
> > gmod_bulk_load_gff3.pl --organism 'Thiobacillus denitrificans ATCC
> > 25259' --gfffile NC_007404.gff --recreate_cache
> >
> > I get the following message:
> >
> > (Re)creating the uniquename cache in the database...
> > Creating table...
> > Populating table...
> > Creating indexes...Done.
> > Preparing data for inserting into the dev_chado_01 database
> > (This may take a while ...)
> > Unable to find srcfeature NC_007404.1 in the database.
> > Perhaps you need to rerun your data load with the '--recreate_cache'
> > option. at /usr/local/share/perl/5.8.8/Bio/GMOD/DB/Adapter.pm line
> > 4026
> >
> >
> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x8bb6808)',
> 'Bio::SeqFeature::Annotated=HASH(0x8c4cd2c)') called at
> /usr/local/bin/gmod_bulk_load_gff3.pl line 758
> > Issuing rollback() for database handle being DESTROY'd without
> > explicit disconnect().
> >
> > This is where I am stuck. Where should I go from here?
> >
> > Victor
> >
> >
> >
> >
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> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         ca...@cs...
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
>
>
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