<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Chao Chao,<div class=""><br class=""></div><div class="">I’m not sure how to trouble shoot this if there were no error messages. I’ve ccd a couple of people that have worked with this protocol much more than I have.</div><div class=""><br class=""></div><div class="">Ning and Kevin,</div><div class="">Do you have any tips for running these tools that may help Chao Chao?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike</div><div class=""><div><blockquote type="cite" class=""><div class="">On Mar 15, 2017, at 8:48 AM, <a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span class=""></span>Thank for your reply!</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">I just followed the guide iat <span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""></span><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced" microsoft="" yahei="" ui'";="" font-size:="" 14px;="" font-weight:="" normal;="" font-style:="" normal;'="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced</a><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">To use LTRHarvest, my command is as below(the filename was set for my favor)</span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><pre style="font-family: monospace, Courier; padding: 1em; border: 1px dashed rgb(47, 111, 171); background-color: rgb(249, 249, 249); line-height: 1.3em; font-size: 12.8px; orphans: 2; widows: 2;" class="">DIR1/gt suffixerator -db seqfile -indexname seqfileindex -tis -suf -lcp -des -ssp –dna</pre></span></div><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: '} ';" class=""></span><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""></span><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><pre style="font-family: monospace, Courier; padding: 1em; border: 1px dashed rgb(47, 111, 171); background-color: rgb(249, 249, 249); line-height: 1.3em; font-size: 12.8px; orphans: 2; widows: 2;" class="">DIR1/gt ltrharvest -index seqfileindex -out seqfile.out99 -outinner seqfile.outinner99 -gff3 seqfile.gff99 -minlenltr 100 \
-maxlenltr 6000 -mindistltr 1500 -maxdistltr 25000 -mintsd 5 -maxtsd 5 -motif tgca -similar 99 -vic 10 > seqfile.result99</pre></div><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">No error, but no results as well</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Chao Chao</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><hr size="1" align="left" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; width: 210px; height: 1px;" class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span class=""><div style="margin: 10px; font-family: verdana; font-size: 10pt;" class=""><div class=""><span style="font-size: 10pt; line-height: 1.5; background-color: window;" class="">2017.03.15</span></div></div></span></div><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em; font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""> </div><div style="border-style: solid none none; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding: 3pt 0cm 0cm;" class=""><div style="padding: 8px; font-size: 12px; font-family: tahoma; background-color: rgb(239, 239, 239);" class=""><div class=""><b class="">From:</b> <a href="mailto:michael.s.campbell1@gmail.com" class="">Michael Campbell</a></div><div class=""><b class="">Date:</b> 2017-03-15 10:27</div><div class=""><b class="">To:</b> <a href="mailto:dcg@cau.edu.cn" class="">dcg</a></div><div class=""><b class="">CC:</b> <a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel</a></div><div class=""><b class="">Subject:</b> Re: [maker-devel] For help about masking repeats before annotation</div></div></div><div class=""><div class="FoxDiv20170315194320765816" style="word-wrap: break-word; -webkit-line-break: after-white-space;">Hi Chao Chao,<div class=""><br class=""></div><div class="">I’ve not run into this before. Could you post the RepeatModeler command you used?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike<br class=""><div class=""><blockquote type="cite" class="" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div class="">On Mar 5, 2017, at 6:26 AM,<span class="Apple-converted-space"> </span><a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a><span class="Apple-converted-space"> </span>wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class=""></span>Dear sir:</div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> Before the maker opeations, I do repeat masking first on my contigs. </div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> However , when I followed " <span class="" style="font-family: sans-serif; line-height: 1.2em; orphans: 2; widows: 2; background-color: window;"><b class="">Repeat Library Construction-Advanced ", no results generated after I running LTRharvest. So I couldn't do any further.</b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: sans-serif; line-height: 1.2em; orphans: 2; widows: 2; background-color: window;"><b class=""> </b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: sans-serif; line-height: 1.2em; orphans: 2; widows: 2; background-color: window;"><b class=""> </b>When I attempted to follow</span><span class="" style="font-size: 10.5pt; line-height: 1.5; background-color: window;">" </span><span class="" style="font-size: 10.5pt; font-family: sans-serif; line-height: 1.2em; orphans: 2; widows: 2; background-color: window;">Repeat Library Construction-Basic " to run RepeatModeler, a note caused my attention even though RECON can return some results :</span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"> <span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><b class="">NOTE: RepeatScout did not return any models.</b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><b class=""><br class=""></b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><b class=""> Is the situation above normal in masking progress? How can I deal with the problems to make a high-quality repeat library for my assemblied contigs?</b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><b class=""><br class=""></b></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"> Hope to hear from you.</span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"> Best wishes!</span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: sans-serif; font-size: 1.6em; line-height: 1.2em; orphans: 2; widows: 2; background-color: window;"><br class=""></span></div><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Chao Chao</div><hr size="1" align="left" class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; width: 210px; height: 1px;"><div class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class=""><div class="" style="margin: 10px; font-family: verdana; font-size: 10pt;"><div class="">2017.03.05</div></div></span></div><span class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">maker-devel mailing list</span><br class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><a href="mailto:maker-devel@box290.bluehost.com" class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">maker-devel@box290.bluehost.com</a><br class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" class="" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div></div></div></div></blockquote></div></blockquote></div><br class=""></div></body></html>