<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=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 31, 2020, at 11:53 AM, Gagné, Patrick (NRCAN/RNCAN) <<a href="mailto:patrick.gagne@canada.ca" class="">patrick.gagne@canada.ca</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: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" class="">Hi<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve come across a bug while using Maker. I’m trying to annotate a 560Mb Genome and I’m using Snap, GeneMark and Augustus in Maker.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">When Maker is executing the GeneMark command, it just failed (GeneMark Failed) without any error messages, so I’ve decided to debug it myself…So I launched every commands manually and found out that the gmhmm_wrap is causing the issue. The problem is in fact in the prebuild command; it doesn’t do anything (from what I understand, this command is supposed to split the fasta whre there is NNN to prevent GeneMark Crash). My genome got very long stretches of N (up to 14Kb)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">After checking the prebuild help, I’ve found that the command used in gmhmm_wrap is not valid (half the options are not in probuild anymore, probably because of GeneMark updates)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have tried different Probuild (those I could download from GeneMark site, they don’t give older versions except those that come with their program’s versions)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2.16<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2.34<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2.44 (lastest that come with GeneMark ES)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve also tried to edit the gmhmm_wrap script and modify the prebuild command, but even when the fasta are splitted, I got another bug<span class="Apple-converted-space"> </span><b class="">: ERROR: Logic error in getting offset.<span class="Apple-converted-space"> </span></b>I’ve tried to replace the command for the offset extraction, which also worked, but now I got a bug when Maker try to get the ab-initio output :<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">------------- EXCEPTION: Bio::Root::Exception -------------<o:p class=""></o:p></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">MSG: Calling translate without a seq argument!<o:p class=""></o:p></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><o:p class=""> </o:p></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Could you please tell me how to fix this, or tell me what probuild I should use (I will ask the GeneMark support for it)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks in advance<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">P.S<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sorry for my English, It’s not my first language and I’m still learning<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span lang="FR-CA" style="color: rgb(33, 33, 33);" class="">Patrick Gagné</span></b><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span lang="FR-CA" style="color: rgb(33, 33, 33);" class="">Spécialiste en bio-informatique / Bioinformatics specialist</span></b><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class="">Service canadien des forêts / Canadian Forest Service</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class="">Ressources naturelles Canada / Natural Resources Canada</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class="">Gouvernement du Canada / Government of Canada<br class="">Centre de foresterie des Laurentides/Laurentian Forestry Centre<br class="">1055, rue du P.E.P.S.<br class="">C.P. 10380, succ. Sainte-Foy/P.O. Box 10380, Stn. Sainte-Foy<br class="">Québec (Qc) G1V 4C7</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class="">Laboratoire de pathologie forestière</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><span class="Apple-converted-space"> </span></span><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class="">(Local 2.21)</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR-CA" style="font-size: 12pt; color: rgb(33, 33, 33);" class=""><a href="mailto:patrick.gagne@canada.ca" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue;" class="">patrick.gagne@canada.ca</span></a><span class="Apple-converted-space"> </span>/ tel : (418) 648-4443</span><span lang="FR-CA" style="color: rgb(33, 33, 33);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="FR" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></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="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@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="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://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>