[maker-devel] invalid gff3 format issues

[Carson Holt]

Could you put the file in this GFF3 validator to see if anything comes up?
—> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Maybe it’s just PASA.  But I’d like to know there’s no issue being caused by
something else.

Thanks,
Carson


From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Wednesday, February 26, 2014 at 1:05 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>, "<maker-devel at yandell-lab.org>"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] invalid gff3 format issues

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 <http://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-4.5
>>> 3-mRNA-1
>>> chr1    maker    exon    9431698    9431808    .    -    .
>>> ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:697;Parent=maker-chr1-snap-gene-4.5
>>> 3-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=ma
>>> ker-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-4.5
>>> 3-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,m
>>> aker-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-4.5
>>> 3-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,m
>>> aker-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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