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<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have some strange results after I have added non-overlapping predictions that had InterPro domains using the "pred_gff" option and “keep_preds=1”. About 19 genes out of 13,000 total now have a missing start coordinate. I copied an example
below (maker-168-augustus-gene-0.1). This particular gene was not even a non-overlapping prediction and it had proper coordinates before I added the non-overlapping predictions.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Brian<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">168 maker five_prime_UTR 1610 1711 . + . ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 1712 1784 . + 0 ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 1846 1885 . + 2 ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 2042 2145 . + 1 ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 2219 2619 . + 2 ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1<o:p></o:p></p>
<p class="MsoNormal"><span style="background:yellow;mso-highlight:yellow">168 maker gene 6737 . + . ID=maker-168-augustus-gene-0.1;Name=maker-168-augustus-gene-0.1</span><o:p></o:p></p>
<p class="MsoNormal">168 maker mRNA 5531 6737 . + . ID=maker-168-augustus-gene-0.1-mRNA-1;Parent=maker-168-augustus-gene-0.1;Name=maker-168-augustus-gene-0.1-mRNA-1;_AED=0.37;_eAED=0.37;_QI=83|0.6|0.66|1|1|1|6|203|184<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 5531 5635 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3421;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 5692 5802 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3422;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 5880 5964 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3423;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 6024 6087 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3424;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 6193 6314 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3425;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker exon 6384 6737 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3426;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker five_prime_UTR 5531 5613 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 5614 5635 . + 0 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 5692 5802 . + 2 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 5880 5964 . + 2 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 6024 6087 . + 1 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 6193 6314 . + 0 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker CDS 6384 6534 . + 1 ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
<p class="MsoNormal">168 maker three_prime_UTR 6535 6737 . + . ID=maker-168-augustus-gene-0.1-mRNA-1:three_prime_utr;Parent=maker-168-augustus-gene-0.1-mRNA-1<o:p></o:p></p>
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