overview and region tracks can't be rendered.

[Zhang, Hua (NIH/NLM/NCBI) [C]]

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To whom it may concern,

 

This is Hua Zhang from NCBI.  The hapmap site is being hosted at ncbi now and it is currently experiencing lots of such errors:

[Mon Nov  2 13:22:24 2009] -e: Bio::DB::GFF::Featname=ARRAY(0x2b939284e4c0) can't $UNIVERSAL::AUTOLOAD=Bio::DB::GFF::Featname::DESTROY!

 

The Overview and Region tracks could not be rendered.  These are recent errors that started to appear about a week ago and I don’t think the backend db was changed recently.  Could you tell me what might be wrong?  If you need additional info., pls let me know.

 

Thanks,

 

Sincerely,

 

Hua

 

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[Scott Cain-4]

Hi Hua,

Marcela and I looked at the database on Friday and I am pretty sure  
there is a database problem.  You have two entries each for your  
chromosomes.  The GFF for one of them looks like this:

chr1 UCSC sequence 1 247249719 . + . ID=Sequence:chr1

and the other like this:

chr1 ensembl chromosome 1 245522847 . . . ID=chr1;Name=Chr1

I would suggest rebulding your database, using only one of the  
chromosome files (probably the later, from vm_cyto.gff).  Addtionally,  
I would suggest making the ID and Name values the same (chr1 and not  
Chr1 for example), though it isn't clear to me that that might be a  
problem.

Scott

PS I just noticed that the lenghts are different too; hopefully  
everything is mapped to the correct build.


On Nov 2, 2009, at 1:31 PM, Zhang, Hua (NIH/NLM/NCBI) [C] wrote:

> To whom it may concern,
>
> This is Hua Zhang from NCBI.  The hapmap site is being hosted at  
> ncbi now and it is currently experiencing lots of such errors:
> [Mon Nov  2 13:22:24 2009] -e:  
> Bio::DB::GFF::Featname=ARRAY(0x2b939284e4c0) can't  
> $UNIVERSAL::AUTOLOAD=Bio::DB::GFF::Featname::DESTROY!
>
> The Overview and Region tracks could not be rendered.  These are  
> recent errors that started to appear about a week ago and I don’t  
> think the backend db was changed recently.  Could you tell me what  
> might be wrong?  If you need additional info., pls let me know.
>
> Thanks,
>
> Sincerely,
>
> Hua
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





------------------------------------------------------------------------------
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