<html><head><style>
body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
padding:1em;
margin:auto;
background:#fefefe;
}
h1, h2, h3, h4, h5, h6 {
font-weight: bold;
}
h1 {
color: #000000;
font-size: 28pt;
}
h2 {
border-bottom: 1px solid #CCCCCC;
color: #000000;
font-size: 24px;
}
h3 {
font-size: 18px;
}
h4 {
font-size: 16px;
}
h5 {
font-size: 14px;
}
h6 {
color: #777777;
background-color: inherit;
font-size: 14px;
}
hr {
height: 0.2em;
border: 0;
color: #CCCCCC;
background-color: #CCCCCC;
display: inherit;
}
p, blockquote, ul, ol, dl, li, table, pre {
margin: 15px 0;
}
a, a:visited {
color: #4183C4;
background-color: inherit;
text-decoration: none;
}
#message {
border-radius: 6px;
border: 1px solid #ccc;
display:block;
width:100%;
height:60px;
margin:6px 0px;
}
button, #ws {
font-size: 12 pt;
padding: 4px 6px;
border-radius: 5px;
border: 1px solid #bbb;
background-color: #eee;
}
code, pre, #ws, #message {
font-family: Monaco;
font-size: 10pt;
border-radius: 3px;
background-color: #F8F8F8;
color: inherit;
}
code {
border: 1px solid #EAEAEA;
margin: 0 2px;
padding: 0 5px;
}
pre {
border: 1px solid #CCCCCC;
overflow: auto;
padding: 4px 8px;
}
pre > code {
border: 0;
margin: 0;
padding: 0;
}
#ws { background-color: #f8f8f8; }
.bloop_markdown table {
border-collapse: collapse;
font-family: Helvetica, arial, freesans, clean, sans-serif;
color: rgb(51, 51, 51);
font-size: 15px; line-height: 25px;
padding: 0; }
.bloop_markdown table tr {
border-top: 1px solid #cccccc;
background-color: white;
margin: 0;
padding: 0; }
.bloop_markdown table tr:nth-child(2n) {
background-color: #f8f8f8; }
.bloop_markdown table tr th {
font-weight: bold;
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr td {
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr th :first-child, table tr td :first-child {
margin-top: 0; }
.bloop_markdown table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
.bloop_markdown blockquote{
border-left: 4px solid #dddddd;
padding: 0 15px;
color: #777777; }
blockquote > :first-child {
margin-top: 0; }
blockquote > :last-child {
margin-bottom: 0; }
code, pre, #ws, #message {
word-break: normal;
word-wrap: normal;
}
hr {
display: inherit;
}
.bloop_markdown :first-child {
-webkit-margin-before: 0;
}
code, pre, #ws, #message {
font-family: Menlo, Consolas, Liberation Mono, Courier, monospace;
}
.send { color:#77bb77; }
.server { color:#7799bb; }
.error { color:#AA0000; }</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="bloop_markdown"><p>Hi, Chris.</p>
<p>Yes, I did get a response from the RepeatModeler author, Robert Hubley (cc’ed). There’s no public mailing list, as far as I know, so it’s all in private communication.</p>
<p>Yes, RepeatModeler is non-deterministic. I suggested that the random seed be added as a parameter to RepeatModeler, and Robert agreed.</p>
<p>I’m still not sure why the results were so variable (between 5 kbp and 30 kbp annotated as repeats, see table far below). Perhaps it’s because my genome is much smaller (6 Mbp) than the size of the random sample (40 Mbp) that RepeatModeler uses. See immediately below. Robert?</p>
<p>Cheers,<br>
Shaun</p>
<pre><code>RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 6001210 bp ( 5937815 non ambiguous )
- Num Contigs Represented = 38
</code></pre>
<p></p></div><div class="bloop_original_html"><div></div><div>
<style type="text/css">
/*<![CDATA[*/
body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
padding:1em;
margin:auto;
background:#fefefe;
}
h1, h2, h3, h4, h5, h6 {
font-weight: bold;
}
h1 {
color: #000000;
font-size: 28pt;
}
h2 {
border-bottom: 1px solid #CCCCCC;
color: #000000;
font-size: 24px;
}
h3 {
font-size: 18px;
}
h4 {
font-size: 16px;
}
h5 {
font-size: 14px;
}
h6 {
color: #777777;
background-color: inherit;
font-size: 14px;
}
hr {
height: 0.2em;
border: 0;
color: #CCCCCC;
background-color: #CCCCCC;
display: inherit;
}
p, blockquote, ul, ol, dl, li, table, pre {
margin: 15px 0;
}
a, a:visited {
color: #4183C4;
background-color: inherit;
text-decoration: none;
}
#message {
border-radius: 6px;
border: 1px solid #ccc;
display:block;
width:100%;
height:60px;
margin:6px 0px;
}
button, #ws {
font-size: 12 pt;
padding: 4px 6px;
border-radius: 5px;
border: 1px solid #bbb;
background-color: #eee;
}
code, pre, #ws, #message {
font-family: Monaco;
font-size: 10pt;
border-radius: 3px;
background-color: #F8F8F8;
color: inherit;
}
code {
border: 1px solid #EAEAEA;
margin: 0 2px;
padding: 0 5px;
}
pre {
border: 1px solid #CCCCCC;
overflow: auto;
padding: 4px 8px;
}
pre > code {
border: 0;
margin: 0;
padding: 0;
}
#ws { background-color: #f8f8f8; }
.bloop_markdown table {
border-collapse: collapse;
font-family: Helvetica, arial, freesans, clean, sans-serif;
color: rgb(51, 51, 51);
font-size: 15px; line-height: 25px;
padding: 0; }
.bloop_markdown table tr {
border-top: 1px solid #cccccc;
background-color: white;
margin: 0;
padding: 0; }
.bloop_markdown table tr:nth-child(2n) {
background-color: #f8f8f8; }
.bloop_markdown table tr th {
font-weight: bold;
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr td {
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr th :first-child, table tr td :first-child {
margin-top: 0; }
.bloop_markdown table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
.bloop_markdown blockquote{
border-left: 4px solid #dddddd;
padding: 0 15px;
color: #777777; }
blockquote > :first-child {
margin-top: 0; }
blockquote > :last-child {
margin-bottom: 0; }
code, pre, #ws, #message {
word-break: normal;
word-wrap: normal;
}
hr {
display: inherit;
}
.bloop_markdown :first-child {
-webkit-margin-before: 0;
}
code, pre, #ws, #message {
font-family: Menlo, Consolas, Liberation Mono, Courier, monospace;
}
.send { color:#77bb77; }
.server { color:#7799bb; }
.error { color:#AA0000; }
/*]]>*/
</style>
<style type="text/css">
/*<![CDATA[*/
body{font-family:Helvetica,Arial;font-size:13px}
/*]]>*/
</style>
<title></title>
<div class="bloop_markdown">
<p><br></p>
</div>
<div class="bloop_original_html">
<div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">
<br></div>
<br>
<div id="bloop_sign_1438279086337435904" class="bloop_sign">
<div style="font-family:helvetica,arial;font-size:13px">
-- <br>
<a href="http://sjackman.ca/">http://sjackman.ca/</a></div>
</div>
<br>
<p class="airmail_on" style="color:#000;">On 2015-July-30 at
9:28:27 , Fields, Christopher J (<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>)
wrote:</p>
<blockquote type="cite" class="clean_bq">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div><span>Hi Shaun</span>
<div class=""><span><br class=""></span></div>
<div class=""><span>Ever get an answer on this one from the
RepeatMasker folks? I’ve seen (and expect) non-deterministic
results from a few tools but the results shouldn’t change *that*
dramatically.</span></div>
<div class=""><span><br class=""></span></div>
<div class=""><span>chris</span></div>
<div class=""><span><br class=""></span>
<div>
<blockquote type="cite" class="">
<div class=""><span>On Jul 17, 2015, at 3:29 PM, Shaun Jackman
<<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</span></div>
<span><br class="Apple-interchange-newline"></span>
<div class="">
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<p style="margin: 15px 0px; -webkit-margin-before: 0px;" class="">
<span>Hi, Carson.</span></p>
<p style="margin: 15px 0px;" class=""><span>It seems that
RepeatModeler is not deterministic. I run it fives times on the
same sequence and get very different outputs. Two of these five
runs mark<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">atp8</code><span class="Apple-converted-space"> </span>as a repeat, which is why I
have genes blinking in and out of existence. How do folk deal with
this situation? It seems absurd. What’s the cause of the
non-determinism? Random number generator? Threading? Can I get
deterministic behaviour if I set the seed of the random number
generator and use it single-threaded? I don’t see how I can
implement a reproducible pipeline with the situation as it
is.</span></p>
<p style="margin: 15px 0px;" class="">This has become a
RepeatModeler question more than a MAKER question, but I thought
I’d continue this thread that I’d started here.</p>
<table style="margin: 15px 0px; border-collapse: collapse; font-family: Helvetica, arial, freesans, clean, sans-serif; color: rgb(51, 51, 51); font-size: 15px; line-height: 25px; padding: 0px;" class="">
<colgroup style="-webkit-margin-before: 0px;" class="">
<col style="-webkit-margin-before: 0px; text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class="">
<col style="text-align: left;" class=""></colgroup>
<thead class="">
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: white; margin: 0px; padding: 0px; -webkit-margin-before: 0px;" class="">
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">n</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">n:1</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">L50</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">min</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">N80</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">N50</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">N20</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">E-size</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">max</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">sum</th>
<th style="font-weight: bold; border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">name</th>
</tr>
</thead>
<tbody class="">
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: white; margin: 0px; padding: 0px; -webkit-margin-before: 0px;" class="">
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">289</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">7667</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">12403</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">12403</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">9102</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">12403</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">24293</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">RepeatModeler1.fa</td>
</tr>
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: rgb(248, 248, 248); margin: 0px; padding: 0px;" class="">
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">332</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">4023</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">14769</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">14769</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">10920</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">14769</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">21738</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">RepeatModeler2.fa</td>
</tr>
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: white; margin: 0px; padding: 0px;" class="">
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">6</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">244</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">370</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2731</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2731</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1765</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2731</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">4688</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">RepeatModeler3.fa</td>
</tr>
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: rgb(248, 248, 248); margin: 0px; padding: 0px;" class="">
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">10</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">10</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">354</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2114</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">17134</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">17134</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">11354</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">17134</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">30782</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">RepeatModeler4.fa</td>
</tr>
<tr style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); background-color: white; margin: 0px; padding: 0px;" class="">
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; -webkit-margin-before: 0px; text-align: left;" class="">8</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">8</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">3</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">538</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1093</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1750</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2526</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">1706</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">2526</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">10713</td>
<td style="border: 1px solid rgb(204, 204, 204); margin: 0px; padding: 6px 13px; text-align: left;" class="">RepeatModeler5.fa</td>
</tr>
</tbody>
</table>
<p style="margin: 15px 0px;" class="">My command line is</p>
<pre style="margin: 15px 0px; font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(204, 204, 204); overflow: auto; padding: 4px 8px; word-break: normal; word-wrap: normal;" class=""><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 0px; margin: 0px; padding: 0px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class=""> BuildDatabase -name x -engine ncbi x.fa
RepeatModeler -database x
cp -a RM_*/consensi.fa.classified RepeatModeler.fa
</code>
</pre>
<p style="margin: 15px 0px;" class="">I installed the following
software using Homebrew on a Mac.</p>
<pre style="margin: 15px 0px; font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(204, 204, 204); overflow: auto; padding: 4px 8px; word-break: normal; word-wrap: normal;" class=""><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 0px; margin: 0px; padding: 0px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">repeatmodeler 1.0.8
recon 1.07
repeatmasker 4.0.5
repeatscout 1.0.5
rmblast 2.2.28
trf 4.07b
</code>
</pre>
<p style="margin: 15px 0px;" class="">Cheers,<br style="-webkit-margin-before: 0px;" class="">
Shaun</p>
<div style="margin: 15px 0px;" class=""><br class="webkit-block-placeholder"></div>
</div>
<div class="bloop_original_html" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div>
<br class="">
<div id="bloop_sign_1437164329546671872" class="bloop_sign">
<div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__sjackman.ca_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_nPDnO1T0QJPouUTvPgqJAnzEmSq22inN1acNTt8giU&s=w8Bvkrxbl2n5I0ND-mzxVr9HaNYWChqaJ6MhO6F0ojg&e=" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">http://sjackman.ca/</a></div>
</div>
<br class="">
<p class="airmail_on" style="margin: 15px 0px;">On 2015-July-17 at
10:36:50 , Carson Holt (<a href="mailto:carsonhh@gmail.com" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">carsonhh@gmail.com</a>) wrote:</p>
<blockquote type="cite" class="clean_bq" style="margin: 15px 0px;">
<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div class=""></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class="">The subset is actually built of a built of a taxonomy. So
you can extract all repeats for a species or genus for example. If
a term doesn’t match the internal taxonomy, it throughs an
error.</span>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class="">—Carson</span></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span>
<div class="">
<blockquote type="cite" class="" style="margin: 15px 0px;">
<div class="" style="margin-top: 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">On Jul 17, 2015, at
11:24 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">carsonhh@gmail.com</a>>
wrote:</span></div>
<span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="Apple-interchange-newline"></span>
<div class="" style="margin-bottom: 0px;">
<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<span style="margin-top: 0px; margin-bottom: 0px;" class="">Yes. It
takes a the subset of RepBase. If runtime isn’t an issue and you
really want to mask as much as possible, you can also
set model_org=all. Most of whatever else is in RepBase
probably won’t align anywhere, but it may give you marginally
better sensitivity.</span>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class="">—Carson</span></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span></div>
<div class=""><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span>
<div class="">
<blockquote type="cite" class="" style="margin: 15px 0px;">
<div class="" style="margin-top: 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">On Jul 17, 2015, at
11:20 AM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">sjackman@gmail.com</a>>
wrote:</span></div>
<span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="Apple-interchange-newline"></span>
<div class="" style="margin-bottom: 0px;">
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<p class="" style="margin: 15px 0px; -webkit-margin-before: 0px;">
<span style="margin-top: 0px; margin-bottom: 0px;" class="">Hi,
Carson.</span></p>
<p class="" style="margin: 15px 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">I set<span class="Apple-converted-space" style="-webkit-margin-before: 0px;"> </span><code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;">model_org=picea</code>.
I see that it created a new data base in the RepeatModeler
folder<span class="Apple-converted-space"> </span><code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;">Libraries/20140131/picea/specieslib</code>.
What is the effect of the<span class="Apple-converted-space"> </span><code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;">model_org</code><span class="Apple-converted-space"> </span>option?
Does it extract sequences from RepBase that match the
string<span class="Apple-converted-space"> </span><code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;">picea</code>?</span></p>
<p class="" style="margin: 15px 0px;">Cheers,<br class="" style="-webkit-margin-before: 0px;">
Shaun</p>
<div class="" style="margin: 15px 0px;"><br class="webkit-block-placeholder" style="-webkit-margin-before: 0px;"></div>
</div>
<div class="bloop_original_html" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;">
<br class=""></div>
<br class="">
<div id="bloop_sign_1437153523647433984" class="bloop_sign">
<div class="" style="font-family: helvetica, arial; font-size: 13px;">
-- <br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__sjackman.ca_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_nPDnO1T0QJPouUTvPgqJAnzEmSq22inN1acNTt8giU&s=w8Bvkrxbl2n5I0ND-mzxVr9HaNYWChqaJ6MhO6F0ojg&e=" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">
http://sjackman.ca/</a></div>
</div>
<br class="">
<p class="airmail_on" style="margin: 15px 0px;">On 2015-July-17 at
9:40:58 , Carson Holt (<a href="mailto:carsonhh@gmail.com" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">carsonhh@gmail.com</a>)
wrote:</p>
<blockquote type="cite" class="clean_bq" style="margin: 15px 0px;">
<div class="" style="margin-top: 0px;"></div>
<span class="" style="margin-top: 0px; margin-bottom: 0px;">That is
weird.</span>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span></div>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;">One thought though.
When you run MAKER do you supply both rmlib and model_org or
just rmlib? If you are only supplying rmlib, you could try
supplying both together (RepeatMasker will then run twice).
That way some of the edge cases might better be
identified.</span></div>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span></div>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;">—Carson</span></div>
<span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span></div>
<span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span>
<div class="" style="margin-top: 0px;"><span class="" style="margin-top: 0px; margin-bottom: 0px;">On Jul 16, 2015, at 5:25 PM,
Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">sjackman@gmail.com</a>>
wrote:</span></div>
<span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="Apple-interchange-newline"></span>
<p class="" style="margin: 15px 0px; -webkit-margin-before: 0px;">
<span class="" style="margin-top: 0px; margin-bottom: 0px;">Hi,
Carson.</span></p>
<span class="" style="margin-top: 0px; margin-bottom: 0px;">I
removed two small contaminant contigs (~7 kbp) from the assembly
(~6 Mbp), and MAKER found four fewer genes, four copies of the
same <code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;">atp8</code> gene,
but these genes were not in the contaminant contigs.I figured out
that it’s because I’m running RepeatModeler to create
the <code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;">rmlib</code> for
MAKER. When I remove the contaminant contigs, RepeatModeler now
identifies this gene <code class="" style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;">atp8</code> as
being a LTR/Gypsy repeat.</span>
<p class="" style="margin: 15px 0px;"><span class="" style="margin-top: 0px; margin-bottom: 0px;">Any thoughts on why removing
two contigs would cause RepeatModeler to identify new
repeats?</span></p>
<p class="" style="margin: 15px 0px;"><span class="" style="margin-top: 0px; margin-bottom: 0px;">Cheers,<br class="" style="-webkit-margin-before: 0px;">
Shaun</span></p>
<div class="" style="margin: 15px 0px;"><span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="webkit-block-placeholder" style="-webkit-margin-before: 0px;"></span></div>
<div class="bloop_original_html" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<div id="bloop_customfont" class="" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;">
<span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span></div>
<span class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></span>
<div id="bloop_sign_1437087480103544832" class="bloop_sign">
<div class="" style="font-family: helvetica, arial; font-size: 13px;"><span class="" style="margin-top: 0px; margin-bottom: 0px;">-- <br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__sjackman.ca_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_nPDnO1T0QJPouUTvPgqJAnzEmSq22inN1acNTt8giU&s=w8Bvkrxbl2n5I0ND-mzxVr9HaNYWChqaJ6MhO6F0ojg&e=" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">
http://sjackman.ca/</a></span></div>
</div>
</div>
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<div class="" style="-webkit-margin-before: 0px; margin: 15px 0px;"><span class="" style="-webkit-margin-before: 0px; margin-top: 0px; margin-bottom: 0px;"><br class="webkit-block-placeholder" style="-webkit-margin-before: 0px;"></span></div>
</div>
<span class="" style="margin-bottom: 0px; margin-top: 0px;"><span class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<span class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;">
maker-devel mailing list</span><br class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<a href="mailto:maker-devel@box290.bluehost.com" class="" style="color: rgb(65, 131, 196); background-color: rgb(254, 254, 254); text-decoration: none; font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; 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: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_nPDnO1T0QJPouUTvPgqJAnzEmSq22inN1acNTt8giU&s=wxmNdg7G5jjyOcWj3fpiLszJfKS9-jB6k7wssWlT888&e=" class="" style="color: rgb(65, 131, 196); background-color: rgb(254, 254, 254); text-decoration: none; font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; 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><br class="" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<br class=""></span></blockquote>
</div>
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<br class="Apple-interchange-newline" style="-webkit-margin-before: 0px;"></div>
</div>
</blockquote>
</div>
<br class=""></div>
</div>
</div>
</div>
</blockquote>
</div>
<br class=""></div>
</div>
</div>
</blockquote>
</div>
<div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);">
<div style="margin: 15px 0px; -webkit-margin-before: 0px;" class=""><br class="webkit-block-placeholder"></div>
</div>
<span style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);" class="">
<span style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);" class="">
<span style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;" class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a></span><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);" class="">
<span style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254); float: none; display: inline !important;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span><br style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);" class=""></div>
</blockquote>
</div>
<br class=""></div>
</div>
</div>
</blockquote>
</div>
<div class="bloop_markdown"></div>
</div></div><div class="bloop_markdown"><p></p></div></body></html>