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.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, Carson.</p>
<p>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 <code>atp8</code> 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.</p>
<p>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>
<colgroup>
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
<col style="text-align:left;">
</colgroup>
<thead>
<tr>
<th style="text-align:left;">n</th>
<th style="text-align:left;">n:1</th>
<th style="text-align:left;">L50</th>
<th style="text-align:left;">min</th>
<th style="text-align:left;">N80</th>
<th style="text-align:left;">N50</th>
<th style="text-align:left;">N20</th>
<th style="text-align:left;">E-size</th>
<th style="text-align:left;">max</th>
<th style="text-align:left;">sum</th>
<th style="text-align:left;">name</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">6</td>
<td style="text-align:left;">6</td>
<td style="text-align:left;">1</td>
<td style="text-align:left;">289</td>
<td style="text-align:left;">7667</td>
<td style="text-align:left;">12403</td>
<td style="text-align:left;">12403</td>
<td style="text-align:left;">9102</td>
<td style="text-align:left;">12403</td>
<td style="text-align:left;">24293</td>
<td style="text-align:left;">RepeatModeler1.fa</td>
</tr>
<tr>
<td style="text-align:left;">6</td>
<td style="text-align:left;">6</td>
<td style="text-align:left;">1</td>
<td style="text-align:left;">332</td>
<td style="text-align:left;">4023</td>
<td style="text-align:left;">14769</td>
<td style="text-align:left;">14769</td>
<td style="text-align:left;">10920</td>
<td style="text-align:left;">14769</td>
<td style="text-align:left;">21738</td>
<td style="text-align:left;">RepeatModeler2.fa</td>
</tr>
<tr>
<td style="text-align:left;">6</td>
<td style="text-align:left;">6</td>
<td style="text-align:left;">1</td>
<td style="text-align:left;">244</td>
<td style="text-align:left;">370</td>
<td style="text-align:left;">2731</td>
<td style="text-align:left;">2731</td>
<td style="text-align:left;">1765</td>
<td style="text-align:left;">2731</td>
<td style="text-align:left;">4688</td>
<td style="text-align:left;">RepeatModeler3.fa</td>
</tr>
<tr>
<td style="text-align:left;">10</td>
<td style="text-align:left;">10</td>
<td style="text-align:left;">1</td>
<td style="text-align:left;">354</td>
<td style="text-align:left;">2114</td>
<td style="text-align:left;">17134</td>
<td style="text-align:left;">17134</td>
<td style="text-align:left;">11354</td>
<td style="text-align:left;">17134</td>
<td style="text-align:left;">30782</td>
<td style="text-align:left;">RepeatModeler4.fa</td>
</tr>
<tr>
<td style="text-align:left;">8</td>
<td style="text-align:left;">8</td>
<td style="text-align:left;">3</td>
<td style="text-align:left;">538</td>
<td style="text-align:left;">1093</td>
<td style="text-align:left;">1750</td>
<td style="text-align:left;">2526</td>
<td style="text-align:left;">1706</td>
<td style="text-align:left;">2526</td>
<td style="text-align:left;">10713</td>
<td style="text-align:left;">RepeatModeler5.fa</td>
</tr>
</tbody>
</table>
<p>My command line is</p>
<pre><code> BuildDatabase -name x -engine ncbi x.fa
RepeatModeler -database x
cp -a RM_*/consensi.fa.classified RepeatModeler.fa
</code></pre>
<p>I installed the following software using Homebrew on a Mac.</p>
<pre><code>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>Cheers,<br>
Shaun</p>
<p></p></div><div class="bloop_original_html"><style>body{font-family:Helvetica,Arial;font-size:13px}</style><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_1437164329546671872" 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-17 at 10:36:50 , Carson Holt (<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>
<title></title>
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.
<div class=""><br class=""></div>
<div class="">—Carson</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jul 17, 2015, at 11:24 AM, Carson Holt
<<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" 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.
<div class=""><br class=""></div>
<div class="">—Carson</div>
<div class=""><br class="">
<div class=""><br class=""></div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Jul 17, 2015, at 11:20 AM, Shaun Jackman
<<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<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="">
Hi, Carson.</p>
<p style="margin: 15px 0px;" class="">I set<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="">model_org=picea</code>. I see that it created a new data
base in the RepeatModeler folder<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;" class="">Libraries/20140131/picea/specieslib</code>. What is the
effect of the<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;" class="">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 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;" class="">picea</code>?</p>
<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_1437153523647433984" class="bloop_sign">
<div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class="">
<a href="http://sjackman.ca/" 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
9:40:58 , 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=""></div>
<span style="margin-top: 0px; margin-bottom: 0px;" class="">That is
weird.</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="">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 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>
<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>
<span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span>
<div class="" style="margin-top: 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">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 style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="Apple-interchange-newline"></span>
<p class="" style="margin: 15px 0px; -webkit-margin-before: 0px;">
<span style="margin-top: 0px; margin-bottom: 0px;" class="">Hi,
Carson.</span></p>
<span style="margin-top: 0px; margin-bottom: 0px;" class="">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 style="margin-top: 0px; margin-bottom: 0px;" class="">Any thoughts on why
removing two contigs would cause RepeatModeler to identify new
repeats?</span></p>
<p class="" style="margin: 15px 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">Cheers,<br class="" style="-webkit-margin-before: 0px;">
Shaun</span></p>
<div class="" style="margin: 15px 0px;"><span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="webkit-block-placeholder" style="-webkit-margin-before: 0px;"></span></div>
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<span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span></div>
<span style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></span>
<div id="bloop_sign_1437087480103544832" class="bloop_sign">
<div class="" style="font-family: helvetica, arial; font-size: 13px;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">-- <br class="">
<a href="http://sjackman.ca/" class="" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;">
http://sjackman.ca/</a></span></div>
</div>
</div>
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