<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="">1. You have two contigs with the same ID in your assembly (one longer and one shorter).<div class="">2. Your BioPerl index for retrieving the sequence is corrupt somehow. Requires delete of previous output directory before restarting.</div><div class="">3. You are using bad formatted GFF3 as input into maker, and it is somehow not failing right away.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">The fact you get output means that it was able to translate the sequence into protein with CDS etc. So it was not too short for that. Look at the contig line in the GFF3 to get the length of the contig maker is seeing to compare to the feature positions given.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 23, 2017, at 5:40 AM, <a href="mailto:lucile.soler@bils.se" class="">lucile.soler@bils.se</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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<!--StartFragment--><p class="MsoNormal">Hello,<o:p class=""></o:p></p><p class="MsoNormal"><o:p class=""> </o:p>I am using maker3 to annotate a lizard.</p><p class="MsoNormal"><o:p class=""></o:p></p><p class="MsoNormal">The maker part went well but then when I want to do the
functional annotation, it seems that for some contigs maker has created genes
outside of the contig size.<o:p class=""></o:p></p><p class="MsoNormal"><o:p class=""> </o:p>For instance :</p><p class="MsoNormal"><o:p class=""></o:p></p><p class="MsoNormal"><o:p class=""> </o:p>XXX1 maker gene 2 26717 . - . ID=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8</p><p class="MsoNormal"><o:p class=""></o:p></p><p class="MsoNormal">XXX1 maker mRNA 2 26717 . - . ID=maker- XXX1_pilon-augustus-gene-0.8-mRNA-1;Parent=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.8|0.5|1|0.4|0.33|6|5291|105<o:p class=""></o:p></p><p class="MsoNormal">XXX1 maker mRNA 2 26717 . - . ID=maker-XXX1_pilon-augustus-gene-0.8-mRNA-2;Parent=maker-XXX1_pilon-augustus-gene-0.8;Name=maker-XXX1_pilon-augustus-gene-0.8-mRNA-2;_AED=0.08;_eAED=0.08;_QI=0|0.5|0.4|1|0.25|0.4|5|4442|170<o:p class=""></o:p></p><p class="MsoNormal">and the length of the contig is 26696</p><p class="MsoNormal"><o:p class=""></o:p></p><p class="MsoNormal"><o:p class=""> </o:p></p><p class="MsoNormal">Any idea of what could have happened? Have you seen that
already?<o:p class=""></o:p></p><p class="MsoNormal"><o:p class=""> </o:p></p><p class="MsoNormal">Let me know what more information you need to answer. <o:p class=""></o:p></p><p class="MsoNormal">Thank you very much for your help,</p><p class="MsoNormal"><o:p class=""></o:p></p><p class="MsoNormal"><br class=""></p><p class="MsoNormal"><o:p class=""></o:p></p>
<!--EndFragment--><div apple-content-edited="true" class="">
<div style="letter-spacing: 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; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Lucile Soler</div><div class=""><br class=""></div><div class="">PhD in Bioinformatics</div><div class="">Genome Annotation Platform</div><div class="">NBIS (National Bioinformatics Infrastructure Sweden)</div><div class="">mail:lucile.soler@<a href="http://bils.se/" class="">bils.se</a></div></div>
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