[maker-devel] invalid gff3 format issues

[Walter Eckalbar]

Hi Carson,

Thanks, that seems to have mostly resolved the issue.  Oddly enough though,
PASA still complains about the GFF3 file directly from gff3_merge, but if I
first transform it with maker2eval_gtf, then use PASA's
gtf_to_gff3_format.pl script, everything seems to run fine.


On 25 February 2014 20:10, Carson Holt <carsonhh at gmail.com> wrote:

> Could you try version 2.31 (the current version)?  I believe this is
> happening because you are passing in MAKER genes as pred_gff the
> transcripts thus ended up with the same Names and IDs as the genes being
> generated by the MAKER run via SNAP etc.  This shouldn't happen with
> model_gff, and shouldn't happen in 2.31 (IDs and names are generated
> slightly differently in 2.30+).
>
> Thanks,
> Carson
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Tuesday, February 25, 2014 at 7:11 PM
> To: Daniel Ence <dence at genetics.utah.edu>
> Cc: "<maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] invalid gff3 format issues
>
> 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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>>
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