[maker-devel] Duplicated exons

[Michael Nuhn]

Hello Carson!

On 05/13/2013 03:01 PM, Carson Holt wrote:
> Could you send me your maker opts files, the contig that fails, and the
> evidence files you use for that contig.

Thanks for offering your help.

I worked around the problem this morning by removing all exons from the 
training set for which I was getting the error. Now I'm rerunning maker 
and I can't find any gff files at the moment with this problem.

If the problem reappears, I'll send you the files.

Cheers,
Michael.

> Thanks,
> Carson
>
>
>
> On 13-05-10 8:29 PM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>
>> On 05/10/2013 07:08 PM, Carson Holt wrote:
>>> 2.27 from the website download or the SVN devel version?
>>
>> SVN. I checked it out on 19/03/2013.
>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> On 13-05-10 1:35 PM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>>>
>>>> On 05/10/2013 05:25 PM, Carson Holt wrote:
>>>>> Very odd.  Which version of MAEKR are you using.  Are you using GFF3
>>>>> passthrough in the run that generates the duplication?
>>>>
>>>> I am using version 2.27 of maker. I am not using the passthrough
>>>> option.
>>>>
>>>> Cheers,
>>>> Michael.
>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>> On 13-05-10 8:10 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>>>>>
>>>>>> Hello Carson!
>>>>>>
>>>>>> I have been trying to get to the bottom of an error message when
>>>>>> (re)training snap. Snap, or more precisely fathom, was giving me
>>>>>> unclear
>>>>>> error messages about misordered and overlapping exons.
>>>>>>
>>>>>> I have looked into the gff files from which these exons originate and
>>>>>> noticed that a lot of exons in that file were duplicated. For
>>>>>> example I
>>>>>> have found these:
>>>>>>
>>>>>> LSalAtl2s75	maker	exon	186317	186936	.	+	.
>>>>>>
>>>>>>
>>>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:3;Parent=maker-LSalAtl
>>>>>> 2s
>>>>>> 75
>>>>>> -snap-gene-2.15-mRNA-1
>>>>>> LSalAtl2s75	maker	exon	187007	191531	.	+	.
>>>>>>
>>>>>>
>>>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl
>>>>>> 2s
>>>>>> 75
>>>>>> -snap-gene-2.15-mRNA-1
>>>>>>
>>>>>> and then about four hundred lines later there are these:
>>>>>>
>>>>>> LSalAtl2s75	maker	exon	186317	186936	.	+	.
>>>>>>
>>>>>>
>>>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:1;Parent=maker-LSalAtl
>>>>>> 2s
>>>>>> 75
>>>>>> -snap-gene-2.15-mRNA-1
>>>>>> LSalAtl2s75	maker	exon	187007	191531	.	+	.
>>>>>>
>>>>>>
>>>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl
>>>>>> 2s
>>>>>> 75
>>>>>> -snap-gene-2.15-mRNA-1
>>>>>>
>>>>>> which are identical except for the order number after "exon:".
>>>>>>
>>>>>> This seems to have happened to a lot of features in that file.
>>>>>>
>>>>>> How can I avoid this? Or if this is just a rare problem, can I have
>>>>>> maker recompute the gff file without redoing all the computations
>>>>>> again?
>>>>>>
>>>>>> Cheers,
>>>>>> Michael.
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>