[maker-devel] Problem with features going against wrong organism

[Scott Cain]

Hi Shane,

I meant to write you about this last week, but I was traveling and it
slipped my mind.  Anyway, I think you are being bitten by a bug in the
chado bulk loader that I fixed a month or so ago.  Try getting a fresh
checkout of the schema repository.

FYI: the best place to write about this is on the schema mailing list
(gmod-schema at lists.sourceforge.net).

Scott


On Thu, Jan 21, 2010 at 6:11 PM, Shane Brubaker
<SBrubaker at aurorabiofuels.com> wrote:
> Hi, I sent an email earlier about this but didn’t really hear back.
>
>
>
> I dug into the problem more (basically my transcriptome and other tracks
> were not showing up on my test organism).  After looking at the error_log
> and doing some debugging, I confirmed that new tracks I load onto a test
> organism have a srcfeature_id which points to the same scaffold, but on my
> production organism.
>
>
>
> I am definitely typing in the name of the test organism when I do the load
> (I am using chado, gmod_gff3_bulk_load).
>
>
>
> I confirmed that if I change the srcfeature_id in the database, I can now
> see the track.
>
>
>
> So I am wondering if anyone has seen this before?   And what do you
> recommend I do next?  I could:
>
>
>
> 1)      Rebuild my entire system
>
> 2)      Try to debug what is happening (maybe in the load script?)
>
> 3)      Just write a script that fixes the problem by updating the
> src_featureids
>
>
>
> Thanks,
>
> Shane
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research