<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="">Hi Anna,<div class=""><br class=""></div><div class="">The lack of results means you either had no results from SNAP or no evidence supporting results in your run. You can check for SNAP results just by looking for snap_masked features in the GFF3. For evidence, make sure you still provided the protein= and est= files even though you tunred off est2genome/protein2genome.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 13, 2018, at 12:35 AM, Ansie Yssel <<a href="mailto:aejysselansie@gmail.com" class="">aejysselansie@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Dear Carson</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I am subscribed to the Maker list, but for some reason I cannot post a new topic when I view the Forum page. I hope it is OK if I email you directly?</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I am trying to annotate a newly sequenced genome.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I have RNAseq data, a species specific repeat library that was generated with REPET, the unmasked genome, and proteins from a "closley" related species (actually not that close, but my species is the only one in its genus, so I took proteins from another genus in the same family).</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I started by following Support Protocol 1, on page 10 of the article "Genome annotation and Curation using MAKER and MAKER-P" published in Curr Protoc Bioinformatics 48.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">The input that I used for generating the gene models (before training SNAP) was:</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">the est data, my genome and the protein data. I also set est2genome=1 and protein2genome=1. I also used Repeat masking and included my species specific repeat library.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">softmasking was set to 1</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">That output was used to train snap. <br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Then I ran maker in "Gene prediction mode" as outlined on page 11 using the hmm file as input (and setting est2genome=0 and protein2genome=0). Repeat masking was enabled, again using my species specific library.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I trained snap for a second time.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">That output was used as input for Basic Protocol 1 on page 3 of the aforementioned article.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Input for Basic Protocol 1 was:</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">The snap hmm file</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">my unmasked genome</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">the species specific repeat library</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">RNAseq evidence</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">the protein evidence from a close relative</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">softmasking was set to 1</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">est2genome=0</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">protein2genome=0</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">I collected the results as outlined on page 5 of the article.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">However I noticed that there were no Fasta files.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Do you have any idea what could have gone wrong?</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Can I send my log files to you? Thanks in advance for any assistance.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class=""><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr" class=""></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Kind Regards</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent" class="">Anna Yssel</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 12 April 2018 at 10:16, Ansie Yssel <span dir="ltr" class=""><<a href="mailto:aejysselansie@gmail.com" target="_blank" class="">aejysselansie@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 dir="ltr" class=""><div class="">Dear Carson</div><div class=""><br class=""></div><div class="">I am subscribed to the Maker list, but for some reason I cannot post a new topic when I view the Forum page. I hope it is OK if I email you directly?</div><div class=""><br class=""></div><div class="">I am trying to annotate a newly sequenced genome.</div><div class="">I have RNAseq data, a species specific repeat library that was generated with REPET, the unmasked genome, and proteins from a "closley" related species (actually not that close, but my species is the only one in its genus, so I took proteins from another genus in the same family).</div><div class=""><br class=""></div><div class="">I started by following Support Protocol 1, on page 10 of the article "Genome annotation and Curation using MAKER and MAKER-P" published in Curr Protoc Bioinformatics 48.</div><div class=""><br class=""></div><div class="">The input that I used for generating the gene models (before training SNAP) was:</div><div class="">the est data, my genome and the protein data. I also set est2genome=1 and protein2genome=1. I also used Repeat masking and included my species specific repeat library.</div><div class="">softmasking was set to 1</div><div class="">That output was used to train snap. <br class=""></div><div class=""><br class=""></div><div class="">Then I ran maker in "Gene prediction mode" as outlined on page 11 using the hmm file as input (and setting est2genome=0 and protein2genome=0). Repeat masking was enabled, again using my species specific library.</div><div class=""><br class=""></div><div class="">I trained snap for a second time.</div><div class="">That output was used as input for Basic Protocol 1 on page 3 of the aforementioned article.</div><div class="">Input for Basic Protocol 1 was:</div><div class="">The snap hmm file</div><div class="">my unmasked genome</div><div class="">the species specific repeat library</div><div class="">RNAseq evidence</div><div class="">the protein evidence from a close relative</div><div class="">softmasking was set to 1</div><div class="">est2genome=0</div><div class="">protein2genome=0</div><div class=""><br class=""></div><div class="">I collected the results as outlined on page 5 of the article.</div><div class="">However I noticed that there were no Fasta files.</div><div class="">Do you have any idea what could have gone wrong?</div><div class="">Can I send my log files to you? Thanks in advance for any assistance.</div><div class=""><br class=""></div><div class="">Kind Regards</div><div class="">Anna Yssel</div><div class=""><br class=""></div>
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