<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Could you send me your maker control files, one of the contigs this occurs on, and the input gff3 file you are using?<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 17, 2014, at 2:33 PM, Mack, Brian <<a href="mailto:Brian.Mack@ARS.USDA.GOV" class="">Brian.Mack@ARS.USDA.GOV</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Brian<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class="">168 maker gene 6737 . + . ID=maker-168-augustus-gene-0.1;Name=maker-168-augustus-gene-0.1</span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">This electronic message contains information generated by the USDA solely for the intended recipients. 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