==> uploading and displaying maker gff file in gbrowse

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==> uploading and displaying maker gff file in gbrowse

Dieter Best-2
Hello there,

I am having trouble displaying tracks from maker2 in gbrowse1.7. I
tried a number of things already, basically I get a http500 error if I
want to display a track.
I am guessing there is something the matter with the gff file from
maker2. I am not having any problems with other gff3 files, from
assemblers for example,  that I upload.
I used maker2chado.pl and also gmod_bulk_load_gff3.pl, and tried a
combination with gmod_gff3_preprocessor.pl.
Has anybody on this list any experience with that and an idea what's going on?

Thanks a lot in advance for suggestions,

-- Dieter

--
http://www.linkedin.com/in/dieterbest

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Re: ==> uploading and displaying maker gff file in gbrowse

Dieter Best-2
Hello there,

if I use maker2chado.pl on a gff file straight from maker2, I get no
error during the upload phase, but if I want to look at the track I
get a http500 error. The tail of the apache error log is attached.

-- Dieter

On Thu, Jun 10, 2010 at 5:01 PM, Dieter Best <[hidden email]> wrote:

> Hello there,
>
> I am having trouble displaying tracks from maker2 in gbrowse1.7. I
> tried a number of things already, basically I get a http500 error if I
> want to display a track.
> I am guessing there is something the matter with the gff file from
> maker2. I am not having any problems with other gff3 files, from
> assemblers for example,  that I upload.
> I used maker2chado.pl and also gmod_bulk_load_gff3.pl, and tried a
> combination with gmod_gff3_preprocessor.pl.
> Has anybody on this list any experience with that and an idea what's going on?
>
> Thanks a lot in advance for suggestions,
>
> -- Dieter
>
> --
> http://www.linkedin.com/in/dieterbest
>


--
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Re: ==> uploading and displaying maker gff file in gbrowse

Scott Cain
Hi Dieter,

It's odd that you get a 500 error but there is nothing in the end of
your error log that indicates a problem.  Did you turn on DEBUG in one
or more of the Bio::DB::Das::Chado, Segment, or Feature objects?  If
so, DEBUG in the Feature object is not so useful, but in the Chado and
Segment objects is more so.

Also, what version of Bio::DB::Das::Chado are you using?  The most
recent version on CPAN is 0.26, which you should be using.  Also,
sending a sample of your data and your configuration file would
probably help too.

Scott


On Fri, Jun 11, 2010 at 7:01 PM, Dieter Best <[hidden email]> wrote:

> Hello there,
>
> if I use maker2chado.pl on a gff file straight from maker2, I get no
> error during the upload phase, but if I want to look at the track I
> get a http500 error. The tail of the apache error log is attached.
>
> -- Dieter
>
> On Thu, Jun 10, 2010 at 5:01 PM, Dieter Best <[hidden email]> wrote:
>> Hello there,
>>
>> I am having trouble displaying tracks from maker2 in gbrowse1.7. I
>> tried a number of things already, basically I get a http500 error if I
>> want to display a track.
>> I am guessing there is something the matter with the gff file from
>> maker2. I am not having any problems with other gff3 files, from
>> assemblers for example,  that I upload.
>> I used maker2chado.pl and also gmod_bulk_load_gff3.pl, and tried a
>> combination with gmod_gff3_preprocessor.pl.
>> Has anybody on this list any experience with that and an idea what's going on?
>>
>> Thanks a lot in advance for suggestions,
>>
>> -- Dieter
>>
>> --
>> http://www.linkedin.com/in/dieterbest
>>
>
>
>
> --
> http://www.linkedin.com/in/dieterbest
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>



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