Hi Scott, Sheldon's suggestion helped me fix the problem. I was having primary reference type as chromosome in GFF data files which I changed to Sequence to match with conf file, and it worked.
I have one more question, I am drawing xyplot on overview. GFF file worked well earlier but when I have loaded these in MySQL and used mysql adaptor it is just blank. Sample data from GFF files looks like this: NC_004347 CDS bin 1270000 1280000 7 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 320000 330000 9 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 900000 910000 11 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 2760000 2770000 10 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 4430000 4440000 11 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 710000 720000 9 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 1180000 1190000 7 + . ID=NC_004347:CDS;Name=NC_004347:CDS NC_004347 CDS bin 2060000 2070000 11 + . ID=NC_004347:CDS;Name=NC_004347:CDS Any assistance in this regards is appreciated. Thanks, Mustafa Syed. --- Scott Cain <[EMAIL PROTECTED]> wrote: > Hi Mustafa, > > I am curious if Sheldon's suggestion fixed your > problem. It doesn't > feel to me like it should be necessary, assuming you > have a reference > sequence line for your features in GFF, like this: > > NC_009999 . region 1 1000000 . . . > ID=NC_009999 > > However, I'm currently trying to debug behavior like > this right now, so > any information you could provide would be > appreciated. > > Thanks, > Scott > > On Mon, 2008-02-11 at 13:21 -0500, Sheldon McKay > wrote: > > Hi Mustafa, > > > > When I encounter this problem, I usually try > adding a sequence-region > > directive for each reference sequence (with the > absolute start and end > > coordinates), so that a full-length feature of > that name and length > > will be autogenerated when the GFF is processed > for database loading. > > > > ##sequence-region NC_009999 1 1000000 > > > > Sheldon > > > > On Feb 11, 2008 12:31 PM, Syed Mustafa Hussain > <[EMAIL PROTECTED]> wrote: > > > Hi, > > > > > > I recently switched from in-memory to MySQL and > have > > > used bp_seqfeature_load.PLS script to create > and load > > > MySQL tables. > > > > > > Gbrowse interface is giving me the following > error: > > > > > > "The landmark named NC_004347:3359971..3369971 > is not > > > recognized. See the help pages for suggestions" > > > > > > What might be wrong with database causing this > error? > > > > > > Where can I get schema diagram to understand > > > relational database created by above script. > > > > > > Mustafa. > > > > > > > > > > ____________________________________________________________________________________ > > > Never miss a thing. Make Yahoo your home page. > > > http://www.yahoo.com/r/hs > > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > > Defy all challenges. Microsoft(R) Visual Studio > 2008. > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > _______________________________________________ > > > Gmod-gbrowse mailing list > > > [email protected] > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. > [EMAIL PROTECTED] > GMOD Coordinator (http://www.gmod.org/) > 216-392-3087 > Cold Spring Harbor Laboratory > > ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-gbrowse mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
