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

[Xin Huang]

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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