[maker-devel] invalid gff3 format issues

[Walter Eckalbar]

Hi Daniel, those have been uploaded and I'm using version 2.28.

Walter


On 25 February 2014 18:02, Daniel Ence <dence at genetics.utah.edu> wrote:

>  Hi Walter,
>
>  Will you upload the full GFF3 and the control files that you used to
> this URL?
>  http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=189
> Also, what version of MAKER are you running this with?
>
>  Thanks,
> Daniel
>
>
>
>  On Feb 25, 2014, at 6:36 PM, Walter Eckalbar <weckalba at asu.edu>
>  wrote:
>
>   Hi all,
>
> I am trying to update maker annotations with PASA and encountered errors
> stemming from file format issues in the gff3 file.
>
>  I put a few lines from the gff3 to highlight the issue below.  Basically,
> the problem is that there are non-unique IDs for a number of the
> annotations.
>
>  Is there anything that can be done to right this problem?
>
> Thanks,
>
>  Walter
>
> Lines from GFF3 file, repeated IDs are highlighted:
>
>
> chr1    maker    gene    9377440    9432028    .    -    .
> ID=maker-chr1-pred_gff_maker-gene-4.16;Name=maker-chr1-pred_gff_maker-gene-4.16
> chr1    maker    mRNA    9377440    9432028    .    -    .
> ID=maker-chr1-snap-gene-4.53-mRNA-1;
> Parent=maker-chr1-pred_gff_maker-gene-4.16;Name=maker-chr1-snap-gene-4.53-mRNA-1;_AED=0.17;_eAED=0.17;_QI=66|0.88|0.82|1|1|1|28|1680|1234
> chr1    maker    exon    9431899    9432028    .    -    .
> ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:698;Parent=maker-chr1-snap-gene-4.53-mRNA-1
> chr1    maker    exon    9431698    9431808    .    -    .
> ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:697;Parent=maker-chr1-snap-gene-4.53-mRNA-1
>
> chr1    maker    gene    8894975    9021577    .    +    .
> ID=maker-chr1-snap-gene-4.53;Name=maker-chr1-snap-gene-4.53
> chr1    maker    mRNA    8894975    9021577    .    +    .   ID=maker-chr1-snap-gene-4.53-mRNA-1;
> Parent=maker-chr1-snap-gene-4.53;Name=maker-chr1-snap-gene-4.53-mRNA-1;_AED=0.16;_eAED=0.17;_QI=229|0.73|0.74|1|0.84|0.88|27|503|2007
> chr1    maker    exon    8894975    8895153    .    +    .
> ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:558;Parent=maker-chr1-snap-gene-4.53-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,maker-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-snap-gene-4.53-mRNA-6,maker-chr1-snap-gene-4.53-mRNA-7,maker-chr1-snap-gene-4.53-mRNA-8,maker-chr1-snap-gene-4.53-mRNA-9,maker-chr1-snap-gene-4.53-mRNA-10,maker-chr1-snap-gene-4.53-mRNA-11
> chr1    maker    exon    8942215    8942531    .    +    .
> ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:559;Parent=maker-chr1-snap-gene-4.53-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,maker-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-snap-gene-4.53-mRNA-6,maker-chr1-snap-gene-4.53-mRNA-7,maker-chr1-snap-gene-4.53-mRNA-8,maker-chr1-snap-gene-4.53-mRNA-9,maker-chr1-snap-gene-4.53-mRNA-10,maker-chr1-snap-gene-4.53-mRNA-11
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