Hi Dave,<br><br>I got the GFF File from here:<br><div style="text-align: left;"><a href="ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz">ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz</a><br>
<br>There were no fasta sequences in it and the upload script would not work with the fasta file<br>sitting in the same directory so I appended the ##FASTA line and the fasta sequence of<br>Sorghum bicolor into a new file.<br>
<br>I got the fasta sequence here:<br><a href="ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/assembly/Sbi1/sbi1.fasta.gz">ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/assembly/Sbi1/sbi1.fasta.gz</a><br>
</div><br>Is there a table in Chado that I have to modify in order to add Superscaffolds to a genome<br>that is not completely assembled into chromosomes (AKA psuedomolecules)?<br><br>Manny<br><br><br><div class="gmail_quote">
On Thu, Aug 13, 2009 at 6:23 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Manny,<br>
<br>
Did you get the GFF file from<br>
<a href="http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html" target="_blank">http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html</a> ?<br>
<br>
I downloaded <a href="ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz" target="_blank">ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz</a><br>
and it was a GFF2 file, which may cause a problem for the load_gff3<br>
script. Try using ....<br>
<br>
Um, I don't know what you use to load GFF2 into Chado. Does anybody know?<br>
<br>
A second problem: The file I downloaded does not contain "super_10"<br>
anywhere. (I assume that you downloaded one of the others?) However,<br>
I've still got a guess The file I downloaded does not define any<br>
chromosome/contig wide features. You'll need to write a script to<br>
derive the length of each chromosome/contig/scaffold in the file, and<br>
then define GFF2 lines for each, that span the whole length of the<br>
chrom/contig/scaffold.<br>
<br>
Does that make sense?<br>
<br>
Thanks,<br>
<br>
Dave C<br>
<div><div></div><div class="h5"><br>
On Tue, Aug 4, 2009 at 11:06 AM, Manuel J. Torres<<a href="mailto:mjtorres@uga.edu">mjtorres@uga.edu</a>> wrote:<br>
> I get the following error loading my sorted sorghum GFF3<br>
> file (DOE JGI v1.4) into chado using gmod_bulk_load_gff3.pl:<br>
><br>
> "Unable to find srcfeature super_10 in the database."<br><br>
</div></div></blockquote></div><br>