<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=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">If you are running several times, just rerun in the same directory after altering settings. MAKER will reuse old raw data reports as appropriate. The maker_gff option is really just for reannotating from an old maker run where you no longer have the raw files available.</span><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">—Carson</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 2, 2020, at 12:24 PM, Thodoris Danis <<a href="mailto:danis_theo@hotmail.com" class="">danis_theo@hotmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">Hello maker community,</div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">I am annotating a fish genome with Maker 2.31.10, for which I have transcript evidence and proteins from closely related species. I am running maker in several passes and pass the gff output to the nest pass every time here (<blockquote type="cite" style="color: rgb(136, 136, 136); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);" class=""><div style="margin: 0px;" class="">"#-----Re-annotation Using MAKER Derived GFF3<br class=""></div><div style="margin: 0px;" class="">maker_gff= #re-annotate genome based on this gff3 file",</div></blockquote>), is this wrong? and where is the difference running the maker from scratch without re-supplying every time the new gff?</div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">Secondly, in the second round after predictors training, have I to keep <span class="">est2genome=1 , </span><span class="">protein2genome=1, ests and proteins evidence or not?</span></div><div style="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; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><span class="">How do we switch all thesre parameters? </span></div><div 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=""><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">Any input from experienced maker users is welcome<br class=""></div><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">Thank you for your help</div><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><i class="">Θεόδωρος Δανης </i></div><div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-family: calibri, helvetica, sans-serif; font-size: 12pt; background-color: rgba(0, 0, 0, 0);" class=""><i class="">Thodoris Danis</i></span></div></div></div><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@yandell-lab.org" style="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@yandell-lab.org</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://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" style="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://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>