gff3 file loading

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

gff3 file loading

Asma Riyaz
Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma





------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse