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Hi Shaun
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<div class="">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.</div>
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<div class="">chris</div>
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<blockquote type="cite" class="">
<div class="">On Jul 17, 2015, at 3:29 PM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<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="">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.</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>
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<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>
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L50</th>
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min</th>
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N80</th>
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N50</th>
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N20</th>
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E-size</th>
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max</th>
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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>
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<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>
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7667</td>
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12403</td>
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12403</td>
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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>
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<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>
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<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>
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<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>
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<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">
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<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>
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<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;"><span style="margin-top: 0px; margin-bottom: 0px;" class="">
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<div 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.
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</div>
<div class="">—Carson</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="" style="margin: 15px 0px;">
<div class="" style="margin-top: 0px;">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:</div>
<br class="Apple-interchange-newline">
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<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
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="">
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<blockquote type="cite" class="" style="margin: 15px 0px;">
<div class="" style="margin-top: 0px;">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:</div>
<br class="Apple-interchange-newline">
<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;">Hi, Carson.</p>
<p class="" style="margin: 15px 0px;">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>?</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;">
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<div class="" style="font-family: helvetica, arial; font-size: 13px;">-- <br class="">
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<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;">
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<span class="" style="margin-top: 0px; margin-bottom: 0px;">That is weird.</span>
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<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>
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</span></div>
<div class=""><span class="" style="margin-top: 0px; margin-bottom: 0px;">—Carson</span></div>
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<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>
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<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>
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<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>
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