<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">You have an ID collision in the GFF3. Check the gff3 being sent to maker2zff. If you are using GFF3 as input to MAKER, you likely have a non-unique ID's there that are causing the issue in the first place.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 6, 2020, at 11:36 AM, Carneiro,Celine M <<a href="mailto:c143dad@ufl.edu" class="">c143dad@ufl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Hello,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">I am getting the errors gene:multiple_Einit, gene:multiple_Eterm, and exon:overlaps_prev_exon, at just about every gene model. I've ran the first round of maker on a bird genome I'm annotating with no errors and have started the steps to train SNAP. However, after running fathom -categorize, just about every single gene model has the same set of errors. Here is an example from my log file after running fathom -categorize:</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-family: "Courier New", monospace;" class="">MODEL117 1 1 8 - errors(6): gene:multiple_Einit gene:multiple_Eterm exon-7:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon</span><span class=""><br class=""></span><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL851 1 1 100 - errors(78): gene:multiple_Einit gene:multiple_Eterm exon-99:overlaps_prev_exon exon-98:overlaps_prev_exon exon-97:overlaps_prev_exon exon-95:overlaps_prev_exon exon-94:overlaps_prev_exon exon-93:overlaps_prev_exon exon-91:overlaps_prev_exon exon-90:overlaps_prev_exon exon-89:overlaps_prev_exon exon-87:overlaps_prev_exon exon-86:overlaps_prev_exon exon-85:overlaps_prev_exon exon-83:overlaps_prev_exon exon-82:overlaps_prev_exon exon-81:overlaps_prev_exon exon-79:overlaps_prev_exon exon-78:overlaps_prev_exon exon-77:overlaps_prev_exon exon-75:overlaps_prev_exon exon-74:overlaps_prev_exon exon-73:overlaps_prev_exon exon-71:overlaps_prev_exon exon-70:overlaps_prev_exon exon-69:overlaps_prev_exon exon-67:overlaps_prev_exon exon-66:overlaps_prev_exon exon-65:overlaps_prev_exon exon-63:overlaps_prev_exon exon-62:overlaps_prev_exon exon-61:overlaps_prev_exon exon-59:overlaps_prev_exon exon-58:overlaps_prev_exon exon-57:overlaps_prev_exon exon-55:overlaps_prev_exon exon-54:overlaps_prev_exon exon-53:overlaps_prev_exon exon-51:overlaps_prev_exon exon-50:overlaps_prev_exon exon-49:overlaps_prev_exon exon-48:overlaps_prev_exon exon-47:overlaps_prev_exon exon-46:overlaps_prev_exon exon-45:overlaps_prev_exon exon-43:overlaps_prev_exon exon-42:overlaps_prev_exon exon-41:overlaps_prev_exon exon-39:overlaps_prev_exon exon-38:overlaps_prev_exon exon-37:overlaps_prev_exon exon-35:overlaps_prev_exon exon-34:overlaps_prev_exon exon-33:overlaps_prev_exon exon-31:overlaps_prev_exon exon-30:overlaps_prev_exon exon-29:overlaps_prev_exon exon-27:overlaps_prev_exon exon-26:overlaps_prev_exon exon-25:overlaps_prev_exon exon-23:overlaps_prev_exon exon-22:overlaps_prev_exon exon-21:overlaps_prev_exon exon-19:overlaps_prev_exon exon-18:overlaps_prev_exon exon-17:overlaps_prev_exon exon-15:overlaps_prev_exon exon-14:overlaps_prev_exon exon-13:overlaps_prev_exon exon-11:overlaps_prev_exon exon-10:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-2:overlaps_prev_exon exon-1:overlaps_prev_exon</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL190 1 1 39 + errors(35): gene:multiple_Einit gene:multiple_Eterm exon-2:overlaps_prev_exon exon-3:overlaps_prev_exon exon-4:overlaps_prev_exon exon-5:overlaps_prev_exon exon-6:overlaps_prev_exon exon-7:overlaps_prev_exon exon-8:overlaps_prev_exon exon-9:overlaps_prev_exon exon-11:overlaps_prev_exon exon-12:overlaps_prev_exon exon-13:overlaps_prev_exon exon-14:overlaps_prev_exon exon-15:overlaps_prev_exon exon-16:overlaps_prev_exon exon-17:overlaps_prev_exon exon-18:overlaps_prev_exon exon-20:overlaps_prev_exon exon-21:overlaps_prev_exon exon-22:overlaps_prev_exon exon-23:overlaps_prev_exon exon-24:overlaps_prev_exon exon-25:overlaps_prev_exon exon-26:overlaps_prev_exon exon-27:overlaps_prev_exon exon-29:overlaps_prev_exon exon-30:overlaps_prev_exon exon-32:overlaps_prev_exon exon-33:overlaps_prev_exon exon-34:overlaps_prev_exon exon-35:overlaps_prev_exon exon-36:overlaps_prev_exon exon-38:overlaps_prev_exon exon-39:overlaps_prev_exon</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL424 1 1 10 - errors(8): gene:multiple_Einit gene:multiple_Eterm exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL902 1 1 20 - errors(14): gene:multiple_Einit gene:multiple_Eterm exon-19:overlaps_prev_exon exon-18:overlaps_prev_exon exon-17:overlaps_prev_exon exon-15:overlaps_prev_exon exon-13:overlaps_prev_exon exon-11:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL238 1 1 14 - errors(11): gene:multiple_Einit gene:multiple_Eterm exon-13:overlaps_prev_exon exon-12:overlaps_prev_exon exon-11:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">MODEL39 1 1 6 - errors(1): exon-3:overlaps_prev_exon</span><br class=""></div><span style="font-family: "Courier New", monospace;" class="">MODEL119 1 1 10 + errors(8): gene:multiple_Einit gene:multiple_Eterm exon-2:overlaps_prev_exon exon-4:overlaps_prev_exon exon-6:overlaps_prev_exon exon-7:overlaps_prev_exon exon-8:overlaps_prev_exon exon-10:overlaps_prev_exon</span><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class=""><br class=""></span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class="">Furthermore, I checked my genome.ann file and noticed that my Einit and Exon sites are duplicated. For example:</span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class=""><div class=""><span style="font-family: "Courier New", monospace;" class="">>ScdimlH_1004;HRSCAF=1084</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Einit 38730 38677 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 38255 38178 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 38074 38021 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 24755 24717 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 24213 24149 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 23176 23098 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 22037 21961 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 21269 21080 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 20232 20167 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 19742 19704 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14705 14590 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14255 13980 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14169 13980 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 13303 13223 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 13303 13223 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 12782 12639 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 12782 12639 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5761 5592 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5482 5404 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5140 5064 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4951 4750 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4567 4502 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4256 4185 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 3569 3403 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 3157 3076 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 2936 2800 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Eterm 2186 2000 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Einit 38730 38677 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 38255 38178 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 38074 38021 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 24755 24717 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 24213 24149 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 23176 23098 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 22037 21961 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 21269 21080 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 20232 20167 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 19742 19704 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14705 14590 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14255 13980 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 14169 13980 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 13303 13223 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 13303 13223 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 12782 12639 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 12782 12639 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5761 5592 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5482 5404 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 5140 5064 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4951 4750 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4567 4502 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 4256 4185 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 3569 3403 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 3157 3076 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Exon 2936 2800 MODEL851</span><br class=""></div><div class=""><span style="font-family: "Courier New", monospace;" class="">Eterm 2186 2000 MODEL851<br class=""></span></div><span class=""></span><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Any ideas why I'm seeing this duplication? Lastly, any ideas why my exons are overlapping so much? I appreciate any input and please let me know if you require any more information. </div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thank you!</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Celine</div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt;" class=""><font face="Calibri, Helvetica, sans-serif" class=""><span style="color: rgb(117, 123, 128);" class=""></span></font><span style="font-family: "Times New Roman", Times, serif; font-size: 11pt;" class=""></span><font face="Calibri, Helvetica, sans-serif" class=""><span style="color: rgb(117, 123, 128);" class=""></span></font><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 11pt;" class=""><span style="font-family: "Times New Roman", Times, serif;" class=""><br class=""></span></span></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:maker-devel@yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@yandell-lab.org</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></div></body></html>