[maker-devel] Duplicated exons

[Carson Holt]

Ok.

Thanks,
Carson

On 13-05-13 12:30 PM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:

>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-LSalA
>>>>>>>tl
>>>>>>> 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-LSalA
>>>>>>>tl
>>>>>>> 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-LSalA
>>>>>>>tl
>>>>>>> 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-LSalA
>>>>>>>tl
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>