<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="">Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it’s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Please,<div class="">I ran the command line</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">maker2jbrowse muc1_genome_snap2.all.gff</span></div></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class="">The command created some folders. However, at the end it read</div><div class=""><span style="font-family:Menlo;font-size:11px" class="">No reference sequences defined in configuration, nothing to do.</span><br class=""></div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><span style="font-family:Menlo;font-size:11px" class="">Please what does it mean? How can I view it in jbrowse. </span></div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><span style="font-family:Menlo;font-size:11px" class="">Thanks</span></div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><span style="font-family:Menlo;font-size:11px" class=""><br class=""></span></div><div class=""><div class=""><div class="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
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