[maker-devel] invalid gff3 format issues

[Carson Holt]

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-4.1
>> 6;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=mak
>> er-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,mak
>> er-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-sna
>> p-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,ma
>> ker-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,mak
>> er-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-sna
>> p-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,ma
>> ker-chr1-snap-gene-4.53-mRNA-11
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 

_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140225/f87e77c7/attachment-0003.html>