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<p class="MsoNormal"><span lang="FR-CA">Hi<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA"><o:p> </o:p></span></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal">2.16<o:p></o:p></p>
<p class="MsoNormal">2.34<o:p></o:p></p>
<p class="MsoNormal">2.44 (lastest that come with GeneMark ES)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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
<b>: ERROR: Logic error in getting offset. </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></o:p></p>
<p class="MsoNormal"><b>------------- EXCEPTION: Bio::Root::Exception -------------<o:p></o:p></b></p>
<p class="MsoNormal"><b>MSG: Calling translate without a seq argument!<o:p></o:p></b></p>
<p class="MsoNormal"><b><o:p> </o:p></b></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">P.S <o:p></o:p></p>
<p class="MsoNormal">Sorry for my English, It’s not my first language and I’m still learning<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA">Patrick Gagné</span></b><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA">Spécialiste en bio-informatique / Bioinformatics specialist</span></b><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA">Service canadien des forêts / Canadian Forest Service</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA">Ressources naturelles Canada / Natural Resources Canada</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA">Gouvernement du Canada / Government of Canada<br>
Centre de foresterie des Laurentides/Laurentian Forestry Centre<br>
1055, rue du P.E.P.S.<br>
C.P. 10380, succ. Sainte-Foy/P.O. Box 10380, Stn. Sainte-Foy<br>
Québec (Qc) G1V 4C7</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA">Laboratoire de pathologie forestière</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA">
</span><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA">(Local 2.21)</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR-CA" style="font-size:12.0pt;color:#212121;mso-fareast-language:EN-CA"><a href="mailto:patrick.gagne@canada.ca"><span style="color:blue">patrick.gagne@canada.ca</span></a> / tel : (418) 648-4443</span><span lang="FR-CA" style="color:#212121;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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