[maker-devel] Duplicated exons

[Carson Holt]

Could you send me your maker opts files, the contig that fails, and the
evidence files you use for that contig.

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
>>>>
>>>>
>>>
>>
>>
>