[maker-devel] errors in final gff

[Anurag Priyam]

I am sorry. I have updated the gist -
https://gist.github.com/yeban/ffaf5cd419639dd073a7.
1. The first two chunks contain the annotations with duplicate ids. (4 rows)
2. The last chunk contains the annotations that refer to a
non-existent parent. And what looks like an incomplete line of
annotation (I forgot to state this in my original email).

No, I didn't use est_forward. I am not passing in any old data via GFF3.

-- Priyam

On Sat, Jun 21, 2014 at 3:26 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Also note that ID= must be unique. Name= does not have to be, and won't be
> if the same protein or repeat element aligns to more than one location for
> example.
>
> Thanks,
> Carson
>
>
> On 6/20/14, 3:50 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>>did you use est_forward?  Also in the example you showed all the IDs are
>>unique (one says hit and the other hsp in the ID, so they are different)?
>>Could you find the non-uunique IDs causing the error?
>>
>>--Carson
>>
>>
>>On 6/19/14, 2:05 AM, "Anurag Priyam" <anurag08priyam at gmail.com> wrote:
>>
>>>I used est_gff= option, which refers to a GFF file generated by
>>>cufflinks2gff3. The erroneous annotations didn't come from this GFF.
>>>
>>>-- Priyam
>>>
>>>On Thu, Jun 19, 2014 at 3:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> Are you passing in old data via GFF3?
>>>>
>>>> --Carson
>>>>
>>>>
>>>> On 6/18/14, 12:15 PM, "Anurag Priyam" <anurag08priyam at gmail.com> wrote:
>>>>
>>>>>It's version 2.31.
>>>>>
>>>>>-- Priyam
>>>>>
>>>>>On Wed, Jun 18, 2014 at 11:41 PM, Carson Holt <carsonhh at gmail.com>
>>>>>wrote:
>>>>>> What MAKER version are you using?
>>>>>>
>>>>>> --Carson
>>>>>>
>>>>>>
>>>>>> On 6/18/14, 11:44 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:
>>>>>>
>>>>>>>Hi,
>>>>>>>
>>>>>>>I compiled all annotations generated by MAKER into a single GFF file
>>>>>>>using the gff3_merge script distributed with MAKER. While formatting
>>>>>>>this GFF for use with JBrowse, I found a few errors:
>>>>>>>
>>>>>>>1. Three instances where two features were assigned the same id.
>>>>>>>2. One instance where a group of three subfeatures refer to a
>>>>>>>non-existent parent.
>>>>>>>
>>>>>>>Here is the relevant portion of the GFF file:
>>>>>>>https://gist.github.com/yeban/ffaf5cd419639dd073a7
>>>>>>>
>>>>>>>I worked around the issue temporarily for the job at hand, but I am
>>>>>>>left wondering why would these errors creep in.
>>>>>>>
>>>>>>>-- Priyam
>>>>>>>
>>>>>>>_______________________________________________
>>>>>>>maker-devel mailing list
>>>>>>>maker-devel at box290.bluehost.com
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>>r
>>>>>>>g
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
>
>