==> uploading and displaying maker 2 gff files in gbrowse

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

==> uploading and displaying maker 2 gff files 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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: ==> uploading and displaying maker 2 gff files in gbrowse

Scott Cain
Hi Dieter,

If you are getting a 500 error, you should be getting an error message
in your apache error_log; what is it?  Also, I'm not clear on if you
are trying to use any other back end than Chado.  If you could send a
sample of the GFF that is causing the problem and the command used to
load it, that might be helpful too.

Scott


On Thu, Jun 10, 2010 at 8:29 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
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> 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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: ==> uploading and displaying maker 2 gff files in gbrowse

Dieter Best-2
Hi Scott,

I am still trying to get my story straight, but one thing I can tell
you is the following if I run a gff3 validator on the maker output.
This may be more of a maker than a gmod issue.


$ gff3Valid.pl  scaffold129_v1.gff
<a href='http://iowg.brcdevel.org/gff3.html#a_transcript'>ERROR:</a>
Dbxref is a required attribute for mRNA feature types (line 5)
<a href='http://iowg.brcdevel.org/gff3.html#a_transcript'>ERROR:</a>
description is a required attribute for mRNA feature types (line 5)
<a href='http://iowg.brcdevel.org/gff3.html#a_sod'>ERROR:</a> A seqid
(scaffold129) is referenced but not defined in this file
<a href='http://iowg.brcdevel.org/gff3.html#a_gff_ont'>WARNING:</a>
feature ontologies were not checked.
<a href='http://iowg.brcdevel.org/gff3.html#a_gff_ont'>WARNING:</a>
attribute ontologies were not checked.




On Thu, Jun 10, 2010 at 8:55 PM, Scott Cain <[hidden email]> wrote:

> Hi Dieter,
>
> If you are getting a 500 error, you should be getting an error message
> in your apache error_log; what is it?  Also, I'm not clear on if you
> are trying to use any other back end than Chado.  If you could send a
> sample of the GFF that is causing the problem and the command used to
> load it, that might be helpful too.
>
> Scott
>
>
> On Thu, Jun 10, 2010 at 8:29 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
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> 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
>



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: ==> uploading and displaying maker 2 gff files in gbrowse

Scott Cain
Hi Dieter,

I don't know what validator you are using, but Dbxref and descriptions
are not required of mRNA features in the GFF3 spec.  Perhaps you
should try the validator at modencode:

  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Scott




On Fri, Jun 11, 2010 at 3:31 PM, Dieter Best <[hidden email]> wrote:

> Hi Scott,
>
> I am still trying to get my story straight, but one thing I can tell
> you is the following if I run a gff3 validator on the maker output.
> This may be more of a maker than a gmod issue.
>
>
> $ gff3Valid.pl  scaffold129_v1.gff
> <a href='http://iowg.brcdevel.org/gff3.html#a_transcript'>ERROR:</a>
> Dbxref is a required attribute for mRNA feature types (line 5)
> <a href='http://iowg.brcdevel.org/gff3.html#a_transcript'>ERROR:</a>
> description is a required attribute for mRNA feature types (line 5)
> <a href='http://iowg.brcdevel.org/gff3.html#a_sod'>ERROR:</a> A seqid
> (scaffold129) is referenced but not defined in this file
> <a href='http://iowg.brcdevel.org/gff3.html#a_gff_ont'>WARNING:</a>
> feature ontologies were not checked.
> <a href='http://iowg.brcdevel.org/gff3.html#a_gff_ont'>WARNING:</a>
> attribute ontologies were not checked.
>
>
>
>
> On Thu, Jun 10, 2010 at 8:55 PM, Scott Cain <[hidden email]> wrote:
>> Hi Dieter,
>>
>> If you are getting a 500 error, you should be getting an error message
>> in your apache error_log; what is it?  Also, I'm not clear on if you
>> are trying to use any other back end than Chado.  If you could send a
>> sample of the GFF that is causing the problem and the command used to
>> load it, that might be helpful too.
>>
>> Scott
>>
>>
>> On Thu, Jun 10, 2010 at 8:29 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
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> 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
>>
>
>
>
> --
> http://www.linkedin.com/in/dieterbest
>



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse