[maker-devel] Maker annotation file not recognized by gff3toGenePred of UCSC Genome Browser

[Xin Huang]

Thank you very much for your response. Yes, that is the issue, and after it
had been fixed, the file went through the program just fine.

Thanks,

Xin

On Tue, Aug 25, 2015 at 12:51 PM, Carson Holt <carsonhh at gmail.com> wrote:

> You have edited the file in a way that broke it.
> Gene maker-scaffold10370-exonerate_est2genome-gene-0.0 previously had two
> separate transcript sequences (mRNA-1 and mRNA-2).  You have deleted
> mRNA-1, but some of it’s children exons still exist. Notice that some exons
> have two parents, and you have deleted one of the parents without removing
> the parent relationship.
>
> —Carson
>
>
>
> On Aug 20, 2015, at 9:37 AM, Xin Huang <xh33 at georgetown.edu> wrote:
>
> Dear Developer,
>
> I was trying to use a mixed GFF3 file to do some analysis, which includes
> genome-level gene predictions and manually curated annotations. I replaced
> the gene prediction by Maker annotations where appropriate. And a sample of
> the blended GFF3 file is as follows:
>
> scaffold10370 GLEAN mRNA 3918 18376 0.920154 + .
> ID=CCG000529.1;source_id=Aalb_GLEAN_10002648;
> scaffold10370 GLEAN CDS 3918 3983 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 4521 4598 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 17407 17516 . + 0 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 17588 17767 . + 1 Parent=CCG000529.1;
> scaffold10370 GLEAN CDS 18238 18376 . + 1 Parent=CCG000529.1;
> scaffold10370 maker gene 32452 54508 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=AAEL004146
> scaffold10370 maker mRNA 32452 54508 44204 - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;aED=0.00;eAED=0.00;qI=376|1|1|1|0|0|5|316|548
> scaffold10370 maker exon 32452 33011 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:exon:15;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 35140 35388 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 35455 36119 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 36443 36777 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker exon 53979 54508 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker five_prime_UTR 54133 54508 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:five_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 53979 54132 . - 0
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 36443 36777 . - 2
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 35455 36119 . - 0
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 35140 35388 . - 1
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker CDS 32768 33011 . - 1
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
> scaffold10370 maker three_prime_UTR 32452 32767 . - .
> ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:three_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2
>
> This file does not pass the GFF3 online validator from GenomeTools with
> the following error message:
>
> GenomeTools error: Parent
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" on line 1456 in
> file "/var/www/servers/genometools.org/htdocs/cgi-bin/gff3/Aalbo.gff" was
> not defined (via "ID=")
>
> And when I tried to use gff3toGenePred to convert GFF3 to the refflat
> format, I got the following parsing errors (samples):
>
> Can't find annotation record
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-2" referenced by
> "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-1:exon:114" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:118" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:119" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:120" Parent
> attribute
>
> Can't find annotation record
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1" referenced by
> "maker-scaffold16459-exonerate_est2genome-gene-0.0-mRNA-1:exon:121" Parent
> attribute
>
> What could have been the issue in the annotation file or the way I used
> the file? Any feedback will be highly appreciated!
>
> Sincerely,
>
> Xin Huang
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>
>
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