<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>You didn't supply any evidence or HMM files for gene predictors. Just raw assembly data by itself is insufficient for genome annotation.</div><div><br></div><div>Here is some nice documentation for running MAKER --> <a href="http://gmod.org/wiki/MAKER_Tutorial_2012">http://gmod.org/wiki/MAKER_Tutorial_2012</a></div><div>Here is a nice overview of genome annotation ion general --> <a href="http://fasta.bioch.virginia.edu/cshl/pdf/12/ajm12/euk_genome_annotation_review.pdf">http://fasta.bioch.virginia.edu/cshl/pdf/12/ajm12/euk_genome_annotation_review.pdf</a></div><div><br></div><div>Once you've gone through the documentation and examples, if you come across any questions just let us know.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Borhan, Hossein" <<a href="mailto:Hossein.Borhan@AGR.GC.CA">Hossein.Borhan@AGR.GC.CA</a>><br><span style="font-weight:bold">Date: </span> Monday, 18 March, 2013 4:40 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] failed gene prediction<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; "><div><div><div style="font-family: Calibri, sans-serif; ">Hi</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">I have tried maker on a fungus genome of 45 mb with 1/3 being repeat rich. It did not produce any prediction. I am not sure what is causing this. Attached are the STDERR and opts.ctl. I appreciate your help</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">Hossein</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div><div style="color: rgb(0, 0, 0); font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; "><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px; "><br></span></font></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; color: rgb(0, 0, 0); margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></p></div></div></div></div></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>