[Gmod-help] Re: [Gmod-schema] Error loading GFF3 file into chado

[Manuel J. Torres]

Hi Dave,

I got the GFF File from here:
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz

There were no fasta sequences in it and the upload script would not work
with the fasta file
sitting in the same directory so I appended the ##FASTA line and the fasta
sequence of
Sorghum bicolor into a new file.

I got the fasta sequence here:
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/assembly/Sbi1/sbi1.fasta.gz

Is there a table in Chado that I have to modify in order to add
Superscaffolds to a genome
that is not completely assembled into chromosomes (AKA psuedomolecules)?

Manny


On Thu, Aug 13, 2009 at 6:23 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Manny,
>
> Did you get the GFF file from
> http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html ?
>
> I downloaded
> ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz
> and it was a GFF2 file, which may cause a problem for the load_gff3
> script.  Try using ....
>
> Um, I don't know what you use to load GFF2 into Chado.  Does anybody know?
>
> A second problem:  The file I downloaded does not contain "super_10"
> anywhere.  (I assume that you downloaded one of the others?)  However,
> I've still got a guess  The file I downloaded does not define any
> chromosome/contig wide features.   You'll need to write a script to
> derive the length of each chromosome/contig/scaffold in the file, and
> then define GFF2 lines for each, that span the whole length of the
> chrom/contig/scaffold.
>
> Does that make sense?
>
> Thanks,
>
> Dave C
>
> On Tue, Aug 4, 2009 at 11:06 AM, Manuel J. Torres<mjtorres at uga.edu> wrote:
> > I get the following error loading my sorted sorghum GFF3
> > file (DOE JGI v1.4) into chado using gmod_bulk_load_gff3.pl:
> >
> > "Unable to find srcfeature super_10 in the database."
>
>
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