<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><dt style="box-sizing: border-box; font-style: italic; font-weight: 600; margin-top: 16px; padding: 0px;"><span style="font-style: normal; font-weight: normal; background-color: rgba(255, 255, 255, 0);">Here is the relevant part of the format specification —></span></dt><dt style="box-sizing: border-box; font-style: italic; font-weight: 600; margin-top: 16px; padding: 0px;"><span style="background-color: rgba(255, 255, 255, 0);">##FASTA</span></dt><dd style="box-sizing: border-box; margin-left: 0px; margin-bottom: 16px; padding: 0px 16px;"><p style="box-sizing: border-box; margin-bottom: 16px; margin-top: 0px;"><span style="background-color: rgba(255, 255, 255, 0);">This notation indicates that the annotation portion of the file is at an end and that the remainder of the file contains one or more sequences (nucleotide or protein) in FASTA format. This allows features and sequences to be bundled together. All FASTA sequences included in the file must be included together at the end of the file and may not be interspersed with the features lines. Once a ##FASTA section is encountered no other content beyond valid FASTA sequence is allowed.</span></p></dd><div><br></div><div><br></div>—Carson<div><br><div id="AppleMailSignature" dir="ltr">Sent from my iPhone</div><div dir="ltr"><br>On Aug 20, 2019, at 7:16 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr"><meta http-equiv="content-type" content="text/html; charset=utf-8">All fasta entries must occur at the end of the file according to gff3 specification. If a fasta entry is embedded in the middle, you have a corrupt file. If you are trying to merge gff3, files you can use the gff3_merge script. Concatenation via something like “cat” however results in a broken file.<div><br></div><div>—Carson <br><div><br><div id="AppleMailSignature" dir="ltr">Sent from my iPhone</div><div dir="ltr"><br>On Aug 20, 2019, at 2:14 AM, Jacques Dainat <<a href="mailto:jacques.dainat@nbis.se">jacques.dainat@nbis.se</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Dear Carson,</div><div class=""><br class=""></div><div class="">I’m using <span style="font-family: Menlo; font-size: 11px; background-color: rgb(34, 79, 188);" class=""> </span><span style="font-family: Menlo; font-size: 11px; background-color: rgb(34, 79, 188);" class="">maker/3.01.02</span> with open MPI.</div><div class="">I realised that the option <b class="">maker_gff</b> from the <b class="">maker_opts.ctl</b> works great as long as <u class="">no</u> FASTA sequence is embeded in the GFF3 file.</div><div class="">e.g: </div><div class=""><div class="">```</div><div class=""><span style="font-family: Menlo; font-size: 11px; background-color: rgb(34, 79, 188);" class="">###</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">##FASTA</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">>3098|quiver</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">TTTATGGGTTCAGGCGGACCCATGGCGCCGACCATATTTTGAGAGCTGGACGACTCTGTA</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">GGGTTGGGTATTGGCTGATTATTCATTCAAATCCCACGAGTAGCCTAGGAAGTGACGGTC</span></div><div class="">```</div></div><div class="">I ended up with GFF3 files containing fasta sequences in a sequential manner (All contig1 features then the sequence of contig1, all contig2 features then the sequence of contig2, etc… I precise this because we can meet gff3 files where all the sequences are gather at the end of the file). In such case MAKER takes in consideration only the features met before to reach the <u class="">first</u> FASTA sequence in the file. Then it stops to process the file and doesn’t consider the rest of it.</div><div class=""><br class=""></div>I haven’t seen any particular message but my resulting annotation was obviously wrong. Indeed most of the data repeat/alignment/models contained in the gff file haven’t been passed to MAKER. Would it be possible to add a fix to continue to parse a gff file even after meeting a fasta sequence?</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">/Jacques<br class=""><div class="">
<div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">-------------------------------------------------<br class="">Jacques Dainat, Ph.D.<br class="">NBIS (National Bioinformatics Infrastructure Sweden)<br class="">Genome Annotation Service<br class=""><a href="http://nbis.se/about/staff/jacques-dainat" class="">http://nbis.se/about/staff/jacques-dainat</a></div><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><a href="https://github.com/NBISweden/GAAS" class="">https://github.com/NBISweden/GAAS</a></div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><a href="http://nbis.se/" class="">http://nbis.se</a></div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class="">—<span class="Apple-tab-span" style="white-space: pre;"> </span><b class="">Contact</b><span class="Apple-tab-span" style="white-space: pre;"> </span>— <br class=""><b class="">Address</b>: Uppsala University, Biomedicinska Centrum<br class="">Department of Medical Biochemistry Microbiology, Genomics<br class="">Husargatan 3, box 582<br class="">S-75123 Uppsala Sweden<br class=""><b class="">Phone</b>: +46 18 471 46 25</div></div></div>
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