[maker-devel] errors in final gff

[Carson Holt]

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.or
>>>>>g
>>>>
>>>>
>>
>>