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

[Shane Brubaker]

Thanks Scott!

Can you tell me exactly how/what to do to get a fresh checkout of the schema repository?  Is it an update to the actual database or to just the loading script?

Appreciate the help!


-----Original Message-----
From: Scott Cain [mailto:scott at scottcain.net]
Sent: Thursday, January 21, 2010 4:02 PM
To: Shane Brubaker
Cc: GMOD GBrowse List; maker-devel at yandell-lab.org; Wayne Lam
Subject: Re: [maker-devel] Problem with features going against wrong organism

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

This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient.  Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited.  If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.