<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="">Sorry for the slow reply. Your e-mail was marked as spam for some reason by the e-mail list software, and I only review the spam folder on the list server every few weeks.<div class=""><br class=""></div><div class="">The issue is the way you named the contigs in the input assembly fasta file. Example —> scaffold_1_length=72278661</div><div class=""><br class=""></div><div class="">If you would have just had a name like this 'scaffold_1 length=72278661’ it would have been fine (spaces separate IDs from comments in fasta format), but the equals sign becomes part of the name when you use an ‘_’ character and it creates downstream issues. The way things are ordered it looks as if you did some intermediate processing of the file (i.e. not directly from the maker run)? The original MAKER file should have replaced the ‘=‘ sign with a URI escape sequence (string starting with a % sign) to avoid this kind of issue. But the intermediate processing step appears to have removed the URI escape and changed it back to an ‘=‘ sign which because it used to separate Key=Value in GFF3 format is an illegal character to have in GFF3 (escaping is required by the format).</div><div class=""><br class=""></div><div class="">There is an easy way to fix this in your files though.</div><div class=""><br class=""></div><div class="">Run these commands on your files —> </div><div class="">perl -p -e 's/_length=\d+//g’ Corav.Jeff.First1000Lines.gff > Corav.Jeff.First1000Lines.fix.gff</div><div class="">perl -p -e 's/_length=\d+//g’ Corav.Jeff.all.id.map > Corav.Jeff.all.id.fix.map</div><div class=""><br class=""></div><div class="">Then run —> </div><div class="">map_gff_ids Corav.Jeff.all.id.fix.map Corav.Jeff.all.fix.gff</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 2, 2018, at 11:24 AM, Vining, Kelly <<a href="mailto:Kelly.Vining@oregonstate.edu" class="">Kelly.Vining@oregonstate.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’m having an issue with the id mapping part of the maker pipeline. Specifically, when I run the map_gff_ids script, I get no error messages, the script appears to run, but there are no changes to the gff file. This is one of three genomes that I’m currently annotating, and only this one is having this particular problem. I’ve tried to find any suspect characters or anything amiss with the gff file, but can’t see anything. I’ve recreated the map file multiple times, but that doesn’t fix the problem, either.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Here are the commands I used to make the map file and to try to map the ids to the gff:<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class="">maker_map_ids --prefix Corav.Jeff_ --justify 5 Corav.Jeff.all.gff > Corav.Jeff.all.id.map<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">map_gff_ids Corav.Jeff.all.id.map Corav.Jeff.all.gff<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve attached the map file itself, as well as a subset of the gff file.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Any help with this is much appreciated!<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Kelly Vining, Ph.D.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Assistant Professor, Department of Horticulture<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">4071 Agriculture and Life Sciences Bldg<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Oregon State University<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Corvallis, Oregon 97331<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span id="cid:E8C11FCA-CAF3-45F1-9C13-ECA4F38CCD4B@eduroam.utah.edu"><Corav.Jeff.all.id.map></span><span id="cid:8A1587BE-57AD-496E-9969-21304138E430@eduroam.utah.edu"><Corav.Jeff.First1000Lines.gff></span><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></body></html>