<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=""><div class="">The master_datastore_index.log file has a list of failed and finished contigs. You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.</div><div class=""><br class=""></div><div class="">Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it’s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).</div><div class=""><br class=""></div><div class="">You will need to see if you can identify which contig file is truncated and rerun it.</div><div class=""><br class=""></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><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 9, 2017, at 10:42 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="">Hi Carson<div class="">Thanks for the reply</div><div class=""><br class=""></div><div class="">I generated the off with this command <span style="font-family: 'Times New Roman', stixgeneral, serif; font-size: 15.999099731445313px;" class="">gff3_merge –d </span><span style="font-family: 'Times New Roman', stixgeneral, serif; font-size: 15.999099731445313px;" class="">dpp_contig.maker.output/dpp_contig_master_datastore_index.log</span></div><div class=""><span style="font-family: 'Times New Roman', stixgeneral, serif; font-size: 15.999099731445313px;" class=""><br class=""></span></div><div class=""><font face="Times New Roman, stixgeneral, serif" class=""><span style="font-size:15.999099731445313px" class="">I had to rerun browse with the following command</span></font></div><div class=""><font face="Times New Roman, stixgeneral, serif" class=""><span style="font-size:15.999099731445313px" class=""><br class=""></span></font></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 /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Although its showing</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span></p><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">WARNING: No matching features found for mRNA I don't know what it means</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I don't understand what it means</span></div></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class="">Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="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>
<br class=""><div class="gmail_quote">On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" 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=""><div class="h5"><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-8752983405514246806Apple-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="m_-8752983405514246806gmail_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/<wbr class="">profile/Emmanuel_Nnadi/<wbr class="">publications</a></div></div></div></div>
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