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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Dear Colleague,</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">I had encountered an ERROR when I used MAKER to annotate my genome.</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">It is a large plant genome (more than 3Gb). I included a TE (gff) data, one Transcriptome data (fasta),
and three protein sequences (fasta) for the homology annotation. There are, in total, 29 scaffolds. Three scaffolds faced the “ERROR: Failed while processing all repeats,” while the other 26 finished successfully.</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">I have tried the following methods from the online forum. However, I still can’t fix the error.</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"> </span><span lang="EN-GB"><o:p></o:p></span></p>
<ul type="disc">
<li class="MsoListParagraph" style="mso-list:l0 level1 lfo1"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Check the RepeatMasker configuration</span><o:p></o:p></li><li class="MsoListParagraph" style="mso-list:l0 level1 lfo1"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Check the maker_exe.ctl, and set a updated BLAST (ncbi-blast-2.7.1)</span><o:p></o:p></li><li class="MsoListParagraph" style="mso-list:l0 level1 lfo1"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">replace …/maker/lib/Widget/RepeatMasker.pm
<a href="http://gmod.827538.n3.nabble.com/MAKER-v3-ERROR-Failed-while-processing-all-repeats-td4059410.html" target="_top">
<span style="font-size:11.0pt;font-family:"Calibri",sans-serif">http://gmod.827538.n3.nabble.com/MAKER-v3-ERROR-Failed-while-processing-all-repeats-td4059410.html</span></a>
</span><o:p></o:p></li><li class="MsoListParagraph" style="mso-list:l0 level1 lfo1"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">increase the try_count in the maker_opt.ctl</span><o:p></o:p></li></ul>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"> </span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Could you please help me to solve this problem?</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Thank you for reading my email. I look forward to hearing from you.</span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Best wishes and stay healthy,</span><span style="font-size:10.5pt;color:#212121"> </span><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">Wei Xiong<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">PhD candidate | Wageningen University & Research<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">6708 PB Wageningen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">The Netherlands<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:#212121">Email: <a href="mailto:wei.xiong@wur.nl">
<span style="color:#0563C1">wei.xiong@wur.nl</span></a> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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