[maker-devel] Maker: Re-annotation

[Innocent Onsongo]

I upgraded to 2.28 and Maker is not running. Thanks!


On Wed, May 22, 2013 at 9:03 AM, Carson Holt <Carson.Holt at oicr.on.ca> wrote:

>   Are you using MAKER version 2.10? I ask because there is in issue with
> other_gff in that version that has since been fixed.  So if you don't get
> other_gff to pass-through, you will need to upgrade to 2.28 (release date
> is later today coincidentally).
>
>  For the Augustus GFF3 file, the format is a little weird which is
> causing the problem.  They are mRNA features not attached to genes.  Rather
> than build the expected 3 level gene/mRNA/exon structure for these, it is
> simpler just to convert it to the 2 level match/match_part structure.  Just
> convert the 'mRNA' tag to 'match' and all 'exon' tags to 'match_part'.
>  Rename the GFF3 when your done so that it will force rebuild of the GFF3
> database when you run again.
>
>  Thanks,
> Carson
>
>
>
>   From: Innocent Onsongo <onson001 at umn.edu>
> Date: Wednesday, 22 May, 2013 8:47 AM
> To: Barry Moore <barry.utah at gmail.com>
> Cc: <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Maker: Re-annotation
>
>  No. The MAKER produced GFF3 file does not contain any annotations. I
> even tried setting the keep_preds parameter to 1 (keep_preds=1) to see if
> it will pass annotations from the Augustus produced GFF file into the final
> annotation but that didn't work. I have attached the maker_opts.ctl file
> I used together with the first 100 lines of the GFF files it's using. I
> also include the GFF file produced by MAKER (CGS01058First100.gff)
>
>
>
>
> On Tue, May 21, 2013 at 10:43 PM, Barry Moore <barry.utah at gmail.com>wrote:
>
>> Hi Getiria,
>>
>>  Does the MAKER produced GFF3 file contain any annotations at all?  Can
>> you send the first ~100 lines each of the MAKER produced GFF3 file and of
>> the GFF3 files that you passed via maker_opts.ctl?
>>
>>  B
>>
>>   On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:
>>
>>    Maker Development Team,
>>
>>  I am trying to use Maker for re-annotation using  gene predictions from
>> Augustus. We had previously used Augustus for gene prediction but now want
>> to combine these annotations with some EST data. I updated
>> fields maker_opts.ctl  as below
>>
>>  genome=CGS01058.fasta #genome sequence file in fasta format
>> est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT
>> pred_gff=Augustus.gff3 #ab-initio predictions from
>>  other_gff=Promoters.gff3 #promoter annotations
>> other_gff=CpG_Islands.gff3 # CpG island annotations
>>
>>  Maker runs to completion and according to the log file annotation was
>> successful. However, it also gives a "Segmentation fault (core dumped)"
>> message. It does produce a GFF3 file but when I load the GFF3 file into IGV
>> and look it does not contain any of the exon definitions in Augustus.gff3.
>> Am I missing something?
>>
>>  Regards,
>> Getiria
>>
>>  --
>> Getiria Onsongo, Ph.D.
>> Informatics Analyst, Research Informatics Support System
>> Minnesota Supercomputing Institute for Advanced Computational Research
>> University of Minnesota
>> Minneapolis, MN 55455
>> Phone: 612-624-0532
>>   _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>  Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>>
>>
>>
>>
>>
>
>
>  --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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