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<p>Hi Chao Chao,</p>
<p><br>
</p>
<p>I guess you have an extra "\" in your second command. We put that sign there to indicate the entire thing belong to one command (it is too long to put in one row). I suggest you remove the "\" and try again.</p>
<p><br>
</p>
<p>Good luck!</p>
<p><br>
</p>
<p>Ning Jiang<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Michael Campbell <michael.s.campbell1@gmail.com><br>
<b>Sent:</b> Wednesday, March 15, 2017 11:00:13 AM<br>
<b>To:</b> dcg@cau.edu.cn<br>
<b>Cc:</b> maker-devel; Jiang, Ning; Kevin Childs<br>
<b>Subject:</b> Re: [maker-devel] For help about masking repeats before annotation</font>
<div> </div>
</div>
<div>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" microsoftyaheiui??;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 microsoftyaheiui??;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 microsoftyaheiui??;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 microsoftyaheiui??;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 microsoftyaheiui??;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 microsoftyaheiui??;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="">
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<div class=""><span style="font-size: 10pt; line-height: 1.5; background-color: window;" class="">2017.03.15</span></div>
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<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>
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<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>
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Chao Chao</div>
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<div class="">2017.03.05</div>
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<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;">
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