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GitLab

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<h3>

Dylan Aïssi pushed to branch master

at <a href="https://salsa.debian.org/med-team/bolt-lmm">Debian Med / bolt-lmm</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/bolt-lmm/-/commit/9da560f6bb82cfe6655fc9026778f798c6b7c208">9da560f6</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2021-11-19T16:44:26+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.6+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bolt-lmm/-/commit/90191ff407e8e5613bd2391e38f98ccee5e1089c">90191ff4</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2021-11-19T16:44:26+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bolt-lmm/-/commit/b42c8aed651b52acd148ef598c62bc09d238a060">b42c8aed</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2021-11-19T16:44:32+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.3.6+dfsg'

Update to upstream version '2.3.6+dfsg'

with Debian dir fc6aa8dbf1cc4de2856e5d94fe89a859ebbb473e</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bolt-lmm/-/commit/e2e397e73ad89f6e569555a5fb3f757e06e1e8f1">e2e397e7</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2021-11-19T16:46:06+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#4a4984e578e234294ce35dd28ca453b6909e803b">

example/example.log

</a>

</li>

<li class="file-stats">

<a href="#54376838b5671a49d7f427d1f5ae1479180e003c">

example/example_reml2.log

</a>

</li>

<li class="file-stats">

<a href="#3c54164645e82712b60daf11c4b9d91021e2f70c">

src/Bolt.cpp

</a>

</li>

<li class="file-stats">

<a href="#8ccf43d7badb84a070b3d9dd842cc77703c35e1f">

src/BoltMain.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/bolt-lmm/-/compare/0dc498d9c81c89bb8a93069676fc5901f230bd5a...e2e397e73ad89f6e569555a5fb3f757e06e1e8f1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bolt-lmm (2.3.6+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org>  Fri, 19 Nov 2021 16:44:39 +0100</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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1

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">bolt-lmm (2.3.5+dfsg-2) unstable; urgency=medium</span>

</pre>

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2

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Team upload.</span>

</pre>

</td>

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<br>

</li>

<li id="4a4984e578e234294ce35dd28ca453b6909e803b">

<a href="https://salsa.debian.org/med-team/bolt-lmm/-/compare/0dc498d9c81c89bb8a93069676fc5901f230bd5a...e2e397e73ad89f6e569555a5fb3f757e06e1e8f1#4a4984e578e234294ce35dd28ca453b6909e803b"><strong>example/example.log</strong></a>

<hr>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">                      +-----------------------------+</span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">                      |                       ___   |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">                      |   BOLT-LMM, v2.3.<span class="idiff left right">5</span>   /_ /   |</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">                      |   <span class="idiff left">March</span> 2<span class="idiff">0</span>, 2021    <span class="idiff right">  </span>/_/   |</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">                      |   BOLT-LMM, v2.3.<span class="idiff left right">6</span>   /_ /   |</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">                      |   <span class="idiff left">October</span> 2<span class="idiff right">9</span>, 2021    /_/   |</span>

</pre>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">                      |   Po-Ru Loh            //   |</span>

</pre>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">                      |                        /    |</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">                      +-----------------------------+</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,7 +83,7 @@ Reading bed file #1: EUR_subset.bed</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">Total indivs after QC: 373</span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">Total post-QC SNPs: M = 2431</span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">  Variance component 1: 2431 post-QC SNPs (name: 'modelSnps')</span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">Time for SnpData setup = 0.<span class="idiff left right">401493</span> sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Time for SnpData setup = 0.<span class="idiff left right">583185</span> sec</span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">=== Reading phenotype and covariate data ===</span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,13 +115,13 @@ Total independent covariate vectors: Cindep = 4</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">Number of chroms with >= 1 good SNP: 6</span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">Average norm of projected SNPs:           362.015344</span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">Dimension of all-1s proj space (Nused-1): 365</span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">Time for covariate data setup + Bolt initialization = 0.01<span class="idiff left right">99809</span> sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">Time for covariate data setup + Bolt initialization = 0.01<span class="idiff left right">7633</span> sec</span>

</pre>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">Phenotype 1:   N = 366   mean = 0.00450586   std = 1.0273</span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">=== Computing linear regression (LINREG) stats ===</span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">Time for computing LINREG stats = 0.00<span class="idiff left right">401902</span> sec</span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">Time for computing LINREG stats = 0.00<span class="idiff left right">193405</span> sec</span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">=== Estimating variance parameters ===</span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -134,28 +134,28 @@ Estimating MC scaling f_REML at log(delta) = 1.09865, h2 = 0.25...</td>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">  iter 2:  time=0.01  rNorms/orig: (0.01,0.03)  res2s: 791.087..208.371</span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext">  iter 3:  time=0.01  rNorms/orig: (0.002,0.004)  res2s: 791.958..209.121</span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">  Converged at iter 3: rNorms/orig all < CGtol=0.005</span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">  Time breakdown: dgemm = 42.<span class="idiff left">2</span>%, memory/overhead = 57.<span class="idiff right">8</span>%</span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">  Time breakdown: dgemm = 42.<span class="idiff left">9</span>%, memory/overhead = 57.<span class="idiff right">1</span>%</span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">  MCscaling: logDelta = 1.10, h2 = 0.250, f = 0.0583786</span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 4.23869e-05, h2 = 0.5...</span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">  Batch-solving 16 systems of equations using conjugate gradient iteration</span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">  iter 1:  time=0.01  rNorms/orig: (0.2,0.3)  res2s: 157.403..82.5002</span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext">  iter 2:  time=0.01  rNorms/orig: (0.04,0.1)  res2s: 176.427..94.685</span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.01,0.02)  res2s: 178.429..97.6069</span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.004,0.005)  res2s: 178.791..97.8407</span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.01,0.02)  res2s: 178.429..97.6069</span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.004,0.005)  res2s: 178.791..97.8407</span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">  Converged at iter 4: rNorms/orig all < CGtol=0.005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">1.9</span>%, memory/overhead = 5<span class="idiff right">8.1</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">2.3</span>%, memory/overhead = 5<span class="idiff right">7.7</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">  MCscaling: logDelta = 0.00, h2 = 0.500, f = 0.00362986</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = -0.0727959, h2 = 0.518202...</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">  Batch-solving 16 systems of equations using conjugate gradient iteration</span>

</pre>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.2,0.3)  res2s: 140.004..76.2204</span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.04,0.1)  res2s: 158.154..88.1446</span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.01,0.03)  res2s: 160.162..91.1652</span>

</pre>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.004,0.006)  res2s: 160.548..91.4234</span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.0008,0.001)  res2s: 160.575..91.4401</span>

</pre>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.2,0.3)  res2s: 140.004..76.2204</span>

</pre>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.04,0.1)  res2s: 158.154..88.1446</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.01,0.03)  res2s: 160.162..91.1652</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.004,0.006)  res2s: 160.548..91.4234</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.0008,0.001)  res2s: 160.575..91.4401</span>

</pre>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext">  Time breakdown: dgemm = 42.<span class="idiff left">2</span>%, memory/overhead = 57.<span class="idiff right">8</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">  Time breakdown: dgemm = 42.<span class="idiff left">3</span>%, memory/overhead = 57.<span class="idiff right">7</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">  MCscaling: logDelta = -0.07, h2 = 0.518, f = -0.000114364</span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext">Secant iteration for h2 estimation converged in 1 steps</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,7 +163,7 @@ Estimated (pseudo-)heritability: h2g = 0.518</td>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">To more precisely estimate variance parameters and estimate s.e., use --reml</span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext">Variance params: sigma^2_K = 0.539611, logDelta = -0.072796, f = -0.000114364</span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">Time for fitting variance components = 0.0<span class="idiff left right">84334</span>1 sec</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">Time for fitting variance components = 0.0<span class="idiff left right">69738</span>1 sec</span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">=== Computing mixed model assoc stats (inf. model) ===</span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -179,19 +179,19 @@ Each chunk is excluded when testing SNPs belonging to the chunk</td>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">  iter 5:  time=0.01  rNorms/orig: (0.0008,0.002)  res2s: 95.3793..101.413</span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">  iter 6:  time=0.01  rNorms/orig: (0.0003,0.0004)  res2s: 95.381..101.415</span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">  Converged at iter 6: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">  Time breakdown: dgemm = 59.<span class="idiff left">4</span>%, memory/overhead = 40.<span class="idiff right">6</span>%</span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">  Time breakdown: dgemm = 59.<span class="idiff left">8</span>%, memory/overhead = 40.<span class="idiff right">2</span>%</span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">AvgPro: 1.016   AvgRetro: 0.998   Calibration: 1.018 (0.008)   (30 SNPs)</span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">Ratio of medians: 1.020   Median of ratios: 1.015</span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

187

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<td class="new_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext">Time for computing infinitesimal model assoc stats = 0.0<span class="idiff left right">523069</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">Time for computing infinitesimal model assoc stats = 0.0<span class="idiff left right">387118</span> sec</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext">=== Estimating chip LD Scores using 400 indivs ===</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<td class="new_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">WARNING: Only 373 indivs available; using all</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">Reducing sample size to 368 for memory alignment</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<td class="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">Time for estimating chip LD Scores = 0.00<span class="idiff left right">613809</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">Time for estimating chip LD Scores = 0.00<span class="idiff left right">495601</span> sec</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">=== Reading LD Scores for calibration of Bayesian assoc stats ===</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -247,7 +247,7 @@ Dimension of all-1s proj space (Nused-1): 291</td>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext">  iter 5:  time=0.01 for 18 active reps  approxLL diffs: (0.01,0.62)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">  iter 6:  time=0.01 for 11 active reps  approxLL diffs: (0.00,0.71)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">  iter 7:  time=0.01 for  7 active reps  approxLL diffs: (0.00,0.59)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext">  iter 8:  time=0.0<span class="idiff left right">1</span> for  6 active reps  approxLL diffs: (0.00,0.30)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">  iter 8:  time=0.0<span class="idiff left right">0</span> for  6 active reps  approxLL diffs: (0.00,0.30)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">  iter 9:  time=0.00 for  4 active reps  approxLL diffs: (0.01,0.17)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext">  iter 10:  time=0.00 for  3 active reps  approxLL diffs: (0.00,0.09)</span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="plaintext">  iter 11:  time=0.00 for  2 active reps  approxLL diffs: (0.02,0.04)</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,9 +255,9 @@ Dimension of all-1s proj space (Nused-1): 291</td>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">  iter 13:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">  iter 14:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext">  Converged at iter 14: approxLL diffs each have been < LLtol=0.01</span>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">33.3</span>%, memory/overhead = <span class="idiff right">66.7</span>%</span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">28.7</span>%, memory/overhead = <span class="idiff right">71.3</span>%</span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext">Computing predictions on left-out cross-validation fold</span>

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<td class="old_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">Time for computing predictions = 0.006<span class="idiff left right">18505</span> sec</span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">Time for computing predictions = 0.006<span class="idiff left right">06203</span> sec</span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext">Average PVEs obtained by param pairs tested (high to low):</span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"> f2=0.3, p=0.01: 0.126476</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -324,7 +324,7 @@ Dimension of all-1s proj space (Nused-1): 292</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext">  iter 4:  time=0.01 for 18 active reps  approxLL diffs: (0.10,0.68)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext">  iter 5:  time=0.01 for 18 active reps  approxLL diffs: (0.01,0.31)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext">  iter 6:  time=0.01 for 16 active reps  approxLL diffs: (0.00,0.16)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext">  iter 7:  time=0.0<span class="idiff left right">1</span> for  5 active reps  approxLL diffs: (0.00,0.10)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">  iter 7:  time=0.0<span class="idiff left right">0</span> for  5 active reps  approxLL diffs: (0.00,0.10)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext">  iter 8:  time=0.00 for  3 active reps  approxLL diffs: (0.03,0.10)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="plaintext">  iter 9:  time=0.00 for  3 active reps  approxLL diffs: (0.02,0.09)</span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext">  iter 10:  time=0.00 for  3 active reps  approxLL diffs: (0.01,0.07)</span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -342,9 +342,9 @@ Dimension of all-1s proj space (Nused-1): 292</td>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext">  iter 22:  time=0.00 for  1 active reps  approxLL diffs: (0.02,0.02)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext">  iter 23:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">  Converged at iter 23: approxLL diffs each have been < LLtol=0.01</span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">30.2</span>%, memory/overhead = <span class="idiff right">69.8</span>%</span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">22.9</span>%, memory/overhead = <span class="idiff right">77.1</span>%</span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext">Computing predictions on left-out cross-validation fold</span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext">Time for computing predictions = 0.0060<span class="idiff left right">379</span>5 sec</span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">Time for computing predictions = 0.0060<span class="idiff left right">410</span>5 sec</span>

</pre>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="plaintext">Average PVEs obtained by param pairs tested (high to low):</span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext"> f2=0.3, p=0.01: 0.110938</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -413,9 +413,9 @@ Dimension of all-1s proj space (Nused-1): 292</td>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="plaintext">  iter 9:  time=0.00 for  1 active reps  approxLL diffs: (0.03,0.03)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="plaintext">  iter 10:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="plaintext">  Converged at iter 10: approxLL diffs each have been < LLtol=0.01</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">7.8</span>%, memory/overhead = 6<span class="idiff right">2.2</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.4</span>%, memory/overhead = 6<span class="idiff right">7.6</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="plaintext">Computing predictions on left-out cross-validation fold</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left">200</span>89<span class="idiff right">1</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left right">1921</span>89 sec</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

419

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<td class="new_line diff-line-num" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

419

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

420

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<td class="new_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

420

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext">Average PVEs obtained by param pairs tested (high to low):</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

421

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<td class="new_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

421

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext"> f2=0.5, p=0.01: 0.090904</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -487,9 +487,9 @@ Dimension of all-1s proj space (Nused-1): 292</td>

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<td class="old_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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<td class="new_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="plaintext">  iter 30:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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<td class="new_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="plaintext">  iter 31:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

489

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<td class="new_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

489

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="plaintext">  Converged at iter 31: approxLL diffs each have been < LLtol=0.01</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

490

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<td class="new_line diff-line-num old" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">35.2</span>%, memory/overhead = <span class="idiff right">64.8</span>%</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">28.0</span>%, memory/overhead = <span class="idiff right">72.0</span>%</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

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<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="plaintext">Computing predictions on left-out cross-validation fold</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

492

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<td class="new_line diff-line-num old" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left right">20039</span>1 sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left right">1933</span>1 sec</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

</td>

<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="plaintext">Average PVEs obtained by param pairs tested (high to low):</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="plaintext"> f2=0.5, p=0.01: 0.087902</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -539,9 +539,9 @@ Dimension of all-1s proj space (Nused-1): 292</td>

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<td class="old_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

</td>

<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="plaintext">  iter 8:  time=0.00 for  1 active reps  approxLL diffs: (0.02,0.02)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

</td>

<td class="new_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="plaintext">  iter 9:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

</td>

<td class="new_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="plaintext">  Converged at iter 9: approxLL diffs each have been < LLtol=0.01</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

542

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">7.9</span>%, memory/overhead = 6<span class="idiff right">2.1</span>%</span>

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">1.0</span>%, memory/overhead = 6<span class="idiff right">9.0</span>%</span>

</pre>

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543

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543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="plaintext">Computing predictions on left-out cross-validation fold</span>

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544

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<pre style="margin: 0;">-<span id="LC544" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left right">205207</span> sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext">Time for computing predictions = 0.00<span class="idiff left right">192904</span> sec</span>

</pre>

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545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="plaintext"></span>

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546

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="plaintext">Average PVEs obtained by param pairs tested (high to low):</span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="plaintext"> f2=0.5, p=0.01: 0.056417</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -559,7 +559,7 @@ Detailed CV fold results:</td>

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="plaintext"></span>

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560

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="plaintext">Optimal mixture parameters according to CV: f2 = 0.5, p = 0.01</span>

</pre>

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561

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561

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="plaintext"></span>

</pre>

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562

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<pre style="margin: 0;">-<span id="LC562" class="line" lang="plaintext">Time for estimating mixture parameters = 24.<span class="idiff left right">4375</span> sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext">Time for estimating mixture parameters = 24.<span class="idiff left right">6488</span> sec</span>

</pre>

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563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="plaintext"></span>

</pre>

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564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="plaintext">=== Computing Bayesian mixed model assoc stats with mixture prior ===</span>

</pre>

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565

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565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -567,10 +567,10 @@ Assigning SNPs to 6 chunks for leave-out analysis</td>

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567

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="plaintext">Each chunk is excluded when testing SNPs belonging to the chunk</span>

</pre>

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568

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="plaintext">  Beginning variational Bayes</span>

</pre>

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569

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569

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="plaintext">  iter 1:  time=0.01 for  6 active reps</span>

</pre>

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570

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<pre style="margin: 0;">-<span id="LC570" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">1</span> for  6 active reps  approxLL diffs: (22.70,28.54)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC571" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">1</span> for  6 active reps  approxLL diffs: (1.57,2.82)</span>

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<pre style="margin: 0;">-<span id="LC572" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">1</span> for  6 active reps  approxLL diffs: (0.18,0.58)</span>

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<pre style="margin: 0;">-<span id="LC573" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">1</span> for  6 active reps  approxLL diffs: (0.01,0.18)</span>

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">0</span> for  6 active reps  approxLL diffs: (22.70,28.54)</span>

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">0</span> for  6 active reps  approxLL diffs: (1.57,2.82)</span>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">0</span> for  6 active reps  approxLL diffs: (0.18,0.58)</span>

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">0</span> for  6 active reps  approxLL diffs: (0.01,0.18)</span>

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="plaintext">  iter 6:  time=0.00 for  5 active reps  approxLL diffs: (0.02,0.06)</span>

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="plaintext">  iter 7:  time=0.00 for  5 active reps  approxLL diffs: (0.00,0.05)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="plaintext">  iter 8:  time=0.00 for  1 active reps  approxLL diffs: (0.06,0.06)</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="plaintext">  iter 12:  time=0.00 for  1 active reps  approxLL diffs: (0.02,0.02)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext">  iter 13:  time=0.00 for  1 active reps  approxLL diffs: (0.01,0.01)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext">  Converged at iter 13: approxLL diffs each have been < LLtol=0.01</span>

</pre>

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<pre style="margin: 0;">-<span id="LC583" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">34.2</span>%, memory/overhead = <span class="idiff right">65.8</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext">  Time breakdown: dgemm = <span class="idiff left">27.0</span>%, memory/overhead = <span class="idiff right">73.0</span>%</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="plaintext">Filtering to SNPs with chisq stats, LD Scores, and MAF > 0.01</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="plaintext"># of SNPs passing filters before outlier removal: 2427/2431</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="plaintext">Masking windows around outlier snps (chisq > 20.0)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -590,7 +590,7 @@ Estimated attenuation: 0.428 (0.415)</td>

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590

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590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="plaintext">Intercept of LD Score regression for cur stats: 1.038 (0.044)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

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<td class="new_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

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<pre style="margin: 0;"> <span id="LC591" class="line" lang="plaintext">Calibration factor (ref/cur) to multiply by:      1.003 (0.015)</span>

</pre>

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592

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<td class="new_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

592

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC592" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

593

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<td class="new_line diff-line-num old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC593" class="line" lang="plaintext">Time for computing Bayesian mixed model assoc stats = 0.0<span class="idiff left right">673342</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext">Time for computing Bayesian mixed model assoc stats = 0.0<span class="idiff left right">52876</span> sec</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="new_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC594" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<td class="new_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="plaintext">Calibration stats: mean and lambdaGC (over SNPs used in GRM)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

596

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<td class="new_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

596

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="plaintext">  (note that both should be >1 because of polygenicity)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -599,23 +599,23 @@ Mean BOLT_LMM: 1.0957 (2431 good SNPs)   lambdaGC: 1.06946</td>

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599

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<td class="new_line diff-line-num" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC599" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="plaintext">=== Streaming genotypes to compute and write assoc stats at all SNPs ===</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC601" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

602

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<td class="new_line diff-line-num old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC602" class="line" lang="plaintext">Time for streaming genotypes and writing output = 0.19<span class="idiff left right">0799</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext">Time for streaming genotypes and writing output = 0.19<span class="idiff left right">2738</span> sec</span>

</pre>

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603

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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC603" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="new_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC604" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<td class="new_line diff-line-num" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="plaintext">=== Streaming genotypes to compute and write assoc stats at dosage SNPs ===</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<td class="new_line diff-line-num" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC606" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

607

</td>

<td class="new_line diff-line-num old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC607" class="line" lang="plaintext">Time for streaming dosage genotypes and writing output = 0.0<span class="idiff left right">189848</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">Time for streaming dosage genotypes and writing output = 0.0<span class="idiff left right">329659</span> sec</span>

</pre>

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608

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<td class="new_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC608" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC609" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

</td>

<td class="new_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC610" class="line" lang="plaintext">=== Streaming genotypes to compute and write assoc stats at IMPUTE2 SNPs ===</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

<td class="new_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC611" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

</td>

<td class="new_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC612" class="line" lang="plaintext">Read 379 indivs; using 373 in filtered PLINK data</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

</td>

<td class="new_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC613" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

614

</td>

<td class="new_line diff-line-num old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC614" class="line" lang="plaintext">Time for streaming IMPUTE2 genotypes and writing output = 0.0<span class="idiff left right">20174</span> sec</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">Time for streaming IMPUTE2 genotypes and writing output = 0.0<span class="idiff left right">798271</span> sec</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

</td>

<td class="new_line diff-line-num" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC615" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

</td>

<td class="new_line diff-line-num" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC616" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

</td>

<td class="new_line diff-line-num" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC617" class="line" lang="plaintext">=== Streaming genotypes to compute and write assoc stats at dosage2 SNPs ===</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

</td>

<td class="new_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC618" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

</td>

<td class="new_line diff-line-num old" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC619" class="line" lang="plaintext">Time for streaming dosage2 genotypes and writing output = 0.<span class="idiff left right">042938</span> sec</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext">Time for streaming dosage2 genotypes and writing output = 0.<span class="idiff left right">101125</span> sec</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

</td>

<td class="new_line diff-line-num" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC620" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

621

</td>

<td class="new_line diff-line-num old" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC621" class="line" lang="plaintext">Total elapsed time for analysis = 25.<span class="idiff left right">3461</span> sec</span></pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

621

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext">Total elapsed time for analysis = 25.<span class="idiff left right">8245</span> sec</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="54376838b5671a49d7f427d1f5ae1479180e003c">

<a href="https://salsa.debian.org/med-team/bolt-lmm/-/compare/0dc498d9c81c89bb8a93069676fc5901f230bd5a...e2e397e73ad89f6e569555a5fb3f757e06e1e8f1#54376838b5671a49d7f427d1f5ae1479180e003c"><strong>example/example_reml2.log</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">                      +-----------------------------+</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">                      |                       ___   |</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">                      |   BOLT-LMM, v2.3.<span class="idiff left right">5</span>   /_ /   |</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">                      |   <span class="idiff left">March</span> 2<span class="idiff">0</span>, 2021    <span class="idiff right">  </span>/_/   |</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">                      |   BOLT-LMM, v2.3.<span class="idiff left right">6</span>   /_ /   |</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">                      |   <span class="idiff left">October</span> 2<span class="idiff right">9</span>, 2021    /_/   |</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">                      |   Po-Ru Loh            //   |</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">                      |                        /    |</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">                      +-----------------------------+</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +60,7 @@ Total indivs after QC: 379</td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Total post-QC SNPs: M = 1331</span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">  Variance component 1: 660 post-QC SNPs (name: 'chr21')</span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">  Variance component 2: 671 post-QC SNPs (name: 'chr22')</span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">Time for SnpData setup = 0.3<span class="idiff left right">3790</span>2 sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Time for SnpData setup = 0.3<span class="idiff left right">4543</span>2 sec</span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">=== Reading phenotype and covariate data ===</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +80,7 @@ Total independent covariate vectors: Cindep = 1</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">Number of chroms with >= 1 good SNP: 2</span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">Average norm of projected SNPs:           368.000000</span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">Dimension of all-1s proj space (Nused-1): 368</span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Time for covariate data setup + Bolt initialization = 0.01<span class="idiff left right">2908</span> sec</span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Time for covariate data setup + Bolt initialization = 0.01<span class="idiff left right">15671</span> sec</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">Phenotype 1:   N = 369   mean = -0.000706532   std = 1.02606</span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">Phenotype 2:   N = 369   mean = 1.53117   std = 0.499705</span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,7 +99,7 @@ Estimating MC scaling f_REML at log(delta) = 1.09861, h2 = 0.25...</td>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.001,0.001)  res2s: 874.469..225.607</span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (0.0002,0.0002)  res2s: 874.479..225.61</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">5</span>.7%, memory/overhead = 7<span class="idiff right">4</span>.3%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6</span>.7%, memory/overhead = 7<span class="idiff right">3</span>.3%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">  MCscaling: logDelta = 1.10, h2 = 0.250, f = -0.0414761</span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,7 +109,7 @@ Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125...</td>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">  iter 3:  time=0.00  rNorms/orig: (0.0008,0.001)  res2s: 2350.09..296.683</span>

</pre>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (9e-05,0.0001)  res2s: 2350.11..296.687</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">  Converged at iter 4: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">5.7</span>%, memory/overhead = 7<span class="idiff right">4.3</span>%</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6.3</span>%, memory/overhead = 7<span class="idiff right">3.7</span>%</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">  MCscaling: logDelta = 1.95, h2 = 0.125, f = 0.012255</span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 1.75266, h2 = 0.147712...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,7 +119,7 @@ Estimating MC scaling f_REML at log(delta) = 1.75266, h2 = 0.147712...</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">  iter 3:  time=0.00  rNorms/orig: (0.001,0.002)  res2s: 1888.28..282.578</span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0002,0.0002)  res2s: 1888.31..282.586</span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">  Converged at iter 4: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">  Time breakdown: dgemm = 26.<span class="idiff left">1</span>%, memory/overhead = 73.<span class="idiff right">9</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">  Time breakdown: dgemm = 26.<span class="idiff left">6</span>%, memory/overhead = 73.<span class="idiff right">4</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">  MCscaling: logDelta = 1.75, h2 = 0.148, f = 0.00181293</span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 1.71911, h2 = 0.151986...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -151,14 +151,14 @@ Estimating MC scaling f_REML at log(delta) = 1.71911, h2 = 0.151986...</td>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0004,0.0007)  res2s: 1809.76..293.283</span>

</pre>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (6e-05,9e-05)  res2s: 1809.76..293.283</span>

</pre>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">1.8</span>%, memory/overhead = 6<span class="idiff right">8.2</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.2</span>%, memory/overhead = 6<span class="idiff right">7.8</span>%</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 2.71911, h2 = 0.0618553...</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext">  Batch-solving 8 systems of equations using conjugate gradient iteration</span>

</pre>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.05,0.06)  res2s: 5411.29..341.902</span>

</pre>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (0.003,0.005)  res2s: 5452.11..344.669</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">  iter 3:  time=0.00  rNorms/orig: (0.0002,0.0004)  res2s: 5452.34..344.696</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext">  Converged at iter 3: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">1.8</span>%, memory/overhead = 6<span class="idiff right">8.2</span>%</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.1</span>%, memory/overhead = 6<span class="idiff right">7.9</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext">WARNING: Estimated h2 on leave-out batch 0 exceeds all-SNPs h2</span>

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163

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">         Replacing 0.265571 with 0.151986</span>

</pre>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext">MCscaling:   logDelta[0] = 1.719106,   h2 = 0.152,   Mused = 671  (50.4%)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -180,7 +180,7 @@ Estimating MC scaling f_REML at log(delta) = 1.09861, h2 = 0.25...</td>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.001,0.001)  res2s: 874.469..55.2016</span>

</pre>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (0.0002,0.0002)  res2s: 874.479..55.2022</span>

</pre>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">7.9</span>%, memory/overhead = 7<span class="idiff right">2.1</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6.5</span>%, memory/overhead = 7<span class="idiff right">3.5</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">  MCscaling: logDelta = 1.10, h2 = 0.250, f = -0.103553</span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,7 +190,7 @@ Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125...</td>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext">  iter 3:  time=0.00  rNorms/orig: (0.0008,0.001)  res2s: 2350.09..71.6417</span>

</pre>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (9e-05,0.0001)  res2s: 2350.11..71.6423</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">  Converged at iter 4: rNorms/orig all < CGtol=0.0005</span>

</pre>

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193

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<td class="new_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">7.8</span>%, memory/overhead = 7<span class="idiff right">2.2</span>%</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6.9</span>%, memory/overhead = 7<span class="idiff right">3.1</span>%</span>

</pre>

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194

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<td class="new_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="plaintext">  MCscaling: logDelta = 1.95, h2 = 0.125, f = -0.0587766</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 3.05814, h2 = 0.0448672...</span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,7 +199,7 @@ Estimating MC scaling f_REML at log(delta) = 3.05814, h2 = 0.0448672...</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (0.0007,0.001)  res2s: 7840.59..84.0634</span>

</pre>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext">  iter 3:  time=0.00  rNorms/orig: (4e-05,7e-05)  res2s: 7840.64..84.0642</span>

</pre>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext">  Converged at iter 3: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">7</span>.9%, memory/overhead = 7<span class="idiff right">2</span>.1%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6</span>.9%, memory/overhead = 7<span class="idiff right">3</span>.1%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext">  MCscaling: logDelta = 3.06, h2 = 0.045, f = -0.0246466</span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 3.86133, h2 = 0.0206065...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,7 +207,7 @@ Estimating MC scaling f_REML at log(delta) = 3.86133, h2 = 0.0206065...</td>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.01,0.01)  res2s: 18037.5..88.1625</span>

</pre>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (0.0001,0.0003)  res2s: 18046.2..88.2065</span>

</pre>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">  Time breakdown: dgemm = 27.<span class="idiff left">6</span>%, memory/overhead = 7<span class="idiff right">2.4</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">  Time breakdown: dgemm = 27.<span class="idiff left">0</span>%, memory/overhead = 7<span class="idiff right">3.0</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">  MCscaling: logDelta = 3.86, h2 = 0.021, f = -0.0122715</span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 4.65779, h2 = 0.00939822...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,7 +215,7 @@ Estimating MC scaling f_REML at log(delta) = 4.65779, h2 = 0.00939822...</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.005,0.006)  res2s: 40636.6..90.1814</span>

</pre>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (3e-05,7e-05)  res2s: 40640.7..90.1908</span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">7.6</span>%, memory/overhead = 7<span class="idiff right">2.4</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6.8</span>%, memory/overhead = 7<span class="idiff right">3.2</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">  MCscaling: logDelta = 4.66, h2 = 0.009, f = -0.0057282</span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 5.35504, h2 = 0.00470207...</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -223,7 +223,7 @@ Estimating MC scaling f_REML at log(delta) = 5.35504, h2 = 0.00470207...</td>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.003,0.003)  res2s: 82199.2..91.034</span>

</pre>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (7e-06,2e-05)  res2s: 82201.3..91.0364</span>

</pre>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">7.7</span>%, memory/overhead = 7<span class="idiff right">2.3</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">  Time breakdown: dgemm = 2<span class="idiff left">6.5</span>%, memory/overhead = 7<span class="idiff right">3.5</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">  MCscaling: logDelta = 5.36, h2 = 0.005, f = -0.00257581</span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 5.92476, h2 = 0.00266533...</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -231,7 +231,7 @@ Estimating MC scaling f_REML at log(delta) = 5.92476, h2 = 0.00266533...</td>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.001,0.002)  res2s: 145816..91.405</span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (2e-06,5e-06)  res2s: 145817..91.4057</span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">  Time breakdown: dgemm = 27.<span class="idiff left">8</span>%, memory/overhead = 72.<span class="idiff right">2</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">  Time breakdown: dgemm = 27.<span class="idiff left">1</span>%, memory/overhead = 72.<span class="idiff right">9</span>%</span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext">  MCscaling: logDelta = 5.92, h2 = 0.003, f = -0.00101218</span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="plaintext">WARNING: Secant iteration for h2 estimation may not have converged</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -250,13 +250,13 @@ Estimating MC scaling f_REML at log(delta) = 5.92476, h2 = 0.00266533...</td>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.002,0.003)  res2s: 145671..91.3763</span>

</pre>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (5e-06,9e-06)  res2s: 145674..91.3781</span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3.2</span>%, memory/overhead = 6<span class="idiff right">6.8</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.0</span>%, memory/overhead = 6<span class="idiff right">8.0</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext">Estimating MC scaling f_REML at log(delta) = 6.92476, h2 = 0.000982175...</span>

</pre>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">  Batch-solving 8 systems of equations using conjugate gradient iteration</span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">  iter 1:  time=0.00  rNorms/orig: (0.0008,0.001)  res2s: 397458..91.7015</span>

</pre>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext">  iter 2:  time=0.00  rNorms/orig: (7e-07,1e-06)  res2s: 397459..91.7018</span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext">  Converged at iter 2: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3.4</span>%, memory/overhead = 6<span class="idiff right">6.6</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.5</span>%, memory/overhead = 6<span class="idiff right">7.5</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">MCscaling:   logDelta[0] = 60.456787,   h2 = 0.000,   Mused = 671  (50.4%)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext">WARNING: Estimated h2 on leave-out batch 1 exceeds all-SNPs h2</span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext">         Replacing 0.10913 with 0.00266533</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -279,13 +279,13 @@ Vegs[2][2,2]((0.142948,5.73352e-07),(5.73352e-07,1e-09))</td>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext">Performing initial gradient evaluation</span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext">  Batch-solving 16 systems of equations using conjugate gradient iteration</span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.09,0.1)  res2s: 757.838..714.073</span>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.01,0.02)  res2s: 775.25..735.608</span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.002,0.004)  res2s: 775.947..736.998</span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (0.0002,0.0005)  res2s: 775.968..737.057</span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">1</span>  rNorms/orig: (4e-05,7e-05)  res2s: 775.969..737.058</span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.09,0.1)  res2s: 757.838..714.073</span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">  iter 2:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.01,0.02)  res2s: 775.25..735.608</span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">  iter 3:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.002,0.004)  res2s: 775.947..736.998</span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (0.0002,0.0005)  res2s: 775.968..737.057</span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">0</span>  rNorms/orig: (4e-05,7e-05)  res2s: 775.969..737.058</span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.8</span>%, memory/overhead = 6<span class="idiff right">7.2</span>%</span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">0.2</span>%, memory/overhead = 6<span class="idiff right">9.8</span>%</span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="plaintext">grad[9](3.09407,-6.72961,-1.13849,-3.04818,7.07062,1.17961,13.4749,-2.86227,-7.58339)</span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext">-------------------------------------------------------------------------------</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -299,7 +299,7 @@ Start ITER 1: computing AI matrix</td>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0001,0.0006)  res2s: 391.934..576.579</span>

</pre>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (2e-05,8e-05)  res2s: 391.935..576.579</span>

</pre>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">5.1</span>%, memory/overhead = 6<span class="idiff right">4.9</span>%</span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">2.5</span>%, memory/overhead = 6<span class="idiff right">7.5</span>%</span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext">Reducing off-diagonals by a factor of 4.47035e-08 to make matrix positive definite</span>

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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext">Reducing off-diagonals by a factor of 1.86265e-09 to make matrix positive definite</span>

</pre>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,7 +318,7 @@ Computing actual (approximate) change in log likelihood</td>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="plaintext">  iter 4:  time=0.01  rNorms/orig: (0.001,0.002)  res2s: 760.12..736.003</span>

</pre>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="plaintext">  iter 5:  time=0.01  rNorms/orig: (0.0003,0.0004)  res2s: 760.136..736.026</span>

</pre>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">3.7</span>%, memory/overhead = 5<span class="idiff right">6.3</span>%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">2.9</span>%, memory/overhead = 5<span class="idiff right">7.1</span>%</span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext">grad[9](1.70519,0.912804,1.26463,-4.85099,7.69901,-1.24528,1.75122,0.944023,-5.57033)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext">Approximate change in log likelihood: 0.752385 (attempt 1)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -343,7 +343,7 @@ Start ITER 2: computing AI matrix</td>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0005,0.002)  res2s: 400.293..592.563</span>

</pre>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (9e-05,0.0005)  res2s: 400.305..592.564</span>

</pre>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">1.8</span>%, memory/overhead = 5<span class="idiff right">8.2</span>%</span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">  Time breakdown: dgemm = 4<span class="idiff left">0.5</span>%, memory/overhead = 5<span class="idiff right">9.5</span>%</span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext">Reducing off-diagonals by a factor of 6.51926e-09 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="plaintext">Reducing off-diagonals by a factor of 2.8871e-07 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="plaintext">Reducing off-diagonals by a factor of 8.3819e-09 to make matrix positive definite</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -364,7 +364,7 @@ Computing actual (approximate) change in log likelihood</td>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext">  iter 4:  time=0.01  rNorms/orig: (0.002,0.002)  res2s: 754.521..724.302</span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext">  iter 5:  time=0.01  rNorms/orig: (0.0003,0.0004)  res2s: 754.538..724.327</span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">9.0</span>%, memory/overhead = 6<span class="idiff right">1.0</span>%</span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">6.9</span>%, memory/overhead = 6<span class="idiff right">3.1</span>%</span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext">grad[9](0.0579094,-0.0410736,-0.0340175,-6.19482,7.16577,-2.04715,0.0273764,0.616035,-6.7186)</span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext">Approximate change in log likelihood: 0.0158352 (attempt 1)</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -390,7 +390,7 @@ Start ITER 3: computing AI matrix</td>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (9e-05,0.0005)  res2s: 386.707..577.27</span>

</pre>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="plaintext">  iter 6:  time=0.00  rNorms/orig: (2e-05,9e-05)  res2s: 386.707..577.27</span>

</pre>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="plaintext">  Converged at iter 6: rNorms/orig all < CGtol=0.0005</span>

</pre>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">9.3</span>%, memory/overhead = 6<span class="idiff right">0.7</span>%</span>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">6.8</span>%, memory/overhead = 6<span class="idiff right">3.2</span>%</span>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="plaintext">Reducing off-diagonals by a factor of 1.86265e-09 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="plaintext">Constrained Newton-Raphson optimized variance parameters:</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -413,13 +413,13 @@ Vegs[2][2,2]((0.236845,0.0104505),(0.0104505,0.000461119))</td>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="plaintext">Performing initial gradient evaluation</span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="plaintext">  Batch-solving 101 systems of equations using conjugate gradient iteration</span>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">3</span>  rNorms/orig: (0.1,0.2)  res2s: 649.894..677.471</span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">2</span>  rNorms/orig: (0.1,0.2)  res2s: 649.894..677.471</span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="plaintext">  iter 2:  time=0.02  rNorms/orig: (0.03,0.05)  res2s: 690.393..719.267</span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="plaintext">  iter 3:  time=0.02  rNorms/orig: (0.006,0.01)  res2s: 692.677..723.771</span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext">  iter 4:  time=0.02  rNorms/orig: (0.001,0.002)  res2s: 692.852..724.206</span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext">  iter 5:  time=0.02  rNorms/orig: (0.0002,0.0005)  res2s: 692.865..724.231</span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3</span>.8%, memory/overhead = 6<span class="idiff right">6</span>.2%</span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">0</span>.8%, memory/overhead = 6<span class="idiff right">9</span>.2%</span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext">grad[9](-6.9566,10.7443,-1.85918,-15.0527,20.8568,0.457434,-9.31692,3.14494,-11.8159)</span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="plaintext">-------------------------------------------------------------------------------</span>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (9e-05,0.0005)  res2s: 386.165..577.663</span>

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="plaintext">  iter 6:  time=0.00  rNorms/orig: (2e-05,9e-05)  res2s: 386.166..577.663</span>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="plaintext">  Converged at iter 6: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">7.5</span>%, memory/overhead = 6<span class="idiff right">2.5</span>%</span>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">4.0</span>%, memory/overhead = 6<span class="idiff right">6.0</span>%</span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="plaintext">Reducing off-diagonals by a factor of 3.72529e-09 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="plaintext">Reducing off-diagonals by a factor of 1.11759e-08 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="plaintext">Reducing off-diagonals by a factor of 2.70084e-08 to make matrix positive definite</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -449,13 +449,13 @@ Predicted change in log likelihood: 0.545289</td>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="plaintext">Computing actual (approximate) change in log likelihood</span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="plaintext">  Batch-solving 101 systems of equations using conjugate gradient iteration</span>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">3</span>  rNorms/orig: (0.1,0.2)  res2s: 672.112..720.682</span>

</pre>

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">2</span>  rNorms/orig: (0.1,0.2)  res2s: 672.112..720.682</span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="plaintext">  iter 2:  time=0.03  rNorms/orig: (0.02,0.05)  res2s: 709.603..761.233</span>

</pre>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="plaintext">  iter 3:  time=0.02  rNorms/orig: (0.004,0.009)  res2s: 711.555..765.362</span>

</pre>

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<pre style="margin: 0;">-<span id="LC455" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">3</span>  rNorms/orig: (0.0006,0.002)  res2s: 711.638..765.655</span>

</pre>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">  iter 4:  time=0.0<span class="idiff left right">2</span>  rNorms/orig: (0.0006,0.002)  res2s: 711.638..765.655</span>

</pre>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="plaintext">  iter 5:  time=0.02  rNorms/orig: (0.0001,0.0003)  res2s: 711.643..765.667</span>

</pre>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">4.4</span>%, memory/overhead = 6<span class="idiff right">5.6</span>%</span>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">1.5</span>%, memory/overhead = 6<span class="idiff right">8.5</span>%</span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="plaintext">grad[9](0.593026,-0.656444,0.398117,-8.84248,7.66129,-1.54565,0.982601,-1.77881,-9.57942)</span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="plaintext">Approximate change in log likelihood: 0.505571 (attempt 1)</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -480,7 +480,7 @@ Start ITER 2: computing AI matrix</td>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0004,0.002)  res2s: 448.291..603.825</span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (7e-05,0.0003)  res2s: 448.297..603.826</span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">7.2</span>%, memory/overhead = 6<span class="idiff right">2.8</span>%</span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3.7</span>%, memory/overhead = 6<span class="idiff right">6.3</span>%</span>

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext">Reducing off-diagonals by a factor of 1.55531e-07 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="plaintext">Reducing off-diagonals by a factor of 2.23517e-08 to make matrix positive definite</span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -493,13 +493,13 @@ Predicted change in log likelihood: 0.00319152</td>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="plaintext">Computing actual (approximate) change in log likelihood</span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="plaintext">  Batch-solving 101 systems of equations using conjugate gradient iteration</span>

</pre>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">3</span>  rNorms/orig: (0.1,0.2)  res2s: 669.569..716.126</span>

</pre>

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">  iter 1:  time=0.0<span class="idiff left right">2</span>  rNorms/orig: (0.1,0.2)  res2s: 669.569..716.126</span>

</pre>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="plaintext">  iter 2:  time=0.02  rNorms/orig: (0.02,0.05)  res2s: 707.616..757.118</span>

</pre>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="plaintext">  iter 3:  time=0.02  rNorms/orig: (0.004,0.009)  res2s: 709.676..761.41</span>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="plaintext">  iter 4:  time=0.02  rNorms/orig: (0.0007,0.002)  res2s: 709.767..761.724</span>

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">3</span>  rNorms/orig: (0.0001,0.0003)  res2s: 709.773..761.738</span>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext">  iter 5:  time=0.0<span class="idiff left right">2</span>  rNorms/orig: (0.0001,0.0003)  res2s: 709.773..761.738</span>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3</span>.8%, memory/overhead = 6<span class="idiff right">6</span>.2%</span>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">0</span>.8%, memory/overhead = 6<span class="idiff right">9</span>.2%</span>

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="plaintext">grad[9](0.0132718,0.00120605,-0.000469693,-9.30953,8.31106,-1.85435,-0.0542454,-1.31603,-9.91664)</span>

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="plaintext">Approximate change in log likelihood: 0.00315098 (attempt 1)</span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="plaintext">  iter 4:  time=0.00  rNorms/orig: (0.0004,0.002)  res2s: 444.271..599.25</span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="plaintext">  iter 5:  time=0.00  rNorms/orig: (7e-05,0.0003)  res2s: 444.279..599.251</span>

</pre>

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="plaintext">  Converged at iter 5: rNorms/orig all < CGtol=0.0005</span>

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">7.3</span>%, memory/overhead = 6<span class="idiff right">2.7</span>%</span>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext">  Time breakdown: dgemm = 3<span class="idiff left">3.9</span>%, memory/overhead = 6<span class="idiff right">6.1</span>%</span>

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="plaintext">Constrained Newton-Raphson optimized variance parameters:</span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="plaintext">optVegs[0][2,2]((0.785936,0.0422243),(0.0422243,0.93567))</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -565,4 +565,4 @@ Variance component 2:  "chr22"</td>

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="plaintext">  gen corr (1,2): -0.999999 (53.474367)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="plaintext">  h2g (2,2): 0.000856 (0.090672)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC568" class="line" lang="plaintext">Total elapsed time for analysis = 2.<span class="idiff left right">33954</span> sec</span></pre>

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<td class="old_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext">Total elapsed time for analysis = 2.<span class="idiff left right">2888</span> sec</span></pre>

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<br>

</li>

<li id="3c54164645e82712b60daf11c4b9d91021e2f70c">

<a href="https://salsa.debian.org/med-team/bolt-lmm/-/compare/0dc498d9c81c89bb8a93069676fc5901f230bd5a...e2e397e73ad89f6e569555a5fb3f757e06e1e8f1#3c54164645e82712b60daf11c4b9d91021e2f70c"><strong>src/Bolt.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1264,6 +1264,7 @@ namespace LMM {</td>

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<td class="new_line diff-line-num" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stats</span><span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_SNP_STAT</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1265

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<td class="new_line diff-line-num" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="cpp">    <span class="n" style="color: #333;">covBasis</span><span class="p">.</span><span class="n" style="color: #333;">applyMaskIndivs</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp">    <span class="n" style="color: #333;">covBasis</span><span class="p">.</span><span class="n" style="color: #333;">projectCovars</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1267

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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">phenoNorm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NumericUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">norm2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">Nstride</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="cpp">    <span class="n" style="color: #333;">NumericUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">Nstride</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1268

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<td class="new_line diff-line-num" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// pheno has now been projected and normalized to vector norm 1</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1269

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<td class="new_line diff-line-num" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1270

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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1289,7 +1290,8 @@ namespace LMM {</td>

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<td class="old_line diff-line-num" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1289

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<td class="new_line diff-line-num" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp">      <span class="n" style="color: #333;">pheno</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">residFactor</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1291

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1291

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<td class="new_line diff-line-num" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1292

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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">StatsDataRetroLOCO</span><span class="p">(</span><span class="s" style="color: #d14;">"LINREG"</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pheno</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="cpp">                       <span class="n" style="color: #333;">computeSnpChunkEnds</span><span class="p">(</span><span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp">                       <span class="n" style="color: #333;">computeSnpChunkEnds</span><span class="p">(</span><span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)),</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp">                       <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">residFactor</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">phenoNorm2</span><span class="p">)));</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1295

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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1297

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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2277,7 +2279,7 @@ namespace LMM {</td>

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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"F_MISS"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2280" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">beta_printed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">retroData</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2280" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;">retroData</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">VinvScaleFactors</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// infinitesimal model stat: approx beta, se</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">retroData</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">VinvScaleFactors</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1U</span></span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// infinitesimal model stat: approx beta, se</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BETA"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SE"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="cpp"> <span class="n" style="color: #333;">beta_printed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2340,7 +2342,7 @@ namespace LMM {</td>

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<pre style="margin: 0;"> <span id="LC2342" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">pValueBuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"%.1fE%d"</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">,</span> <span class="n" style="color: #333;">exponent</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2343" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2344" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC2343" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;">retroData</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">VinvScaleFactors</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// infinitesimal model: approx beta, se</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2345" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">retroData</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">VinvScaleFactors</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1U</span></span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// infinitesimal model: approx beta, se</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xPerAlleleVinvPhi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retroData</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">VinvScaleFactors</span><span class="p">[</span><span class="n" style="color: #333;">chunk</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dotProd</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2347" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">BAD_SNP_STAT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">stat</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">xPerAlleleVinvPhi</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">se</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">beta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2352,7 +2354,7 @@ namespace LMM {</td>

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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="cpp">      <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">pValueBuf</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// always output p-value</span></span>

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<pre style="margin: 0;"> <span id="LC2355" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC2356" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">beta_printed</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// special case: linear regression only</span></span>

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<pre style="margin: 0;">-<span id="LC2355" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">BAD_SNP_STAT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">invNorm2</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dotProd</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">BAD_SNP_STAT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">invNorm2</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">dotProd</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">retroData</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">VinvScaleFactors</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2358" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">se</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">beta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="cpp">      <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">se</span><span class="p">;</span>     </span>

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2360

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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="8ccf43d7badb84a070b3d9dd842cc77703c35e1f">

<a href="https://salsa.debian.org/med-team/bolt-lmm/-/compare/0dc498d9c81c89bb8a93069676fc5901f230bd5a...e2e397e73ad89f6e569555a5fb3f757e06e1e8f1#8ccf43d7badb84a070b3d9dd842cc77703c35e1f"><strong>src/BoltMain.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,8 +54,8 @@ int main(int argc, char *argv[]) {</td>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      +-----------------------------+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |                       ___   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

57

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<td class="new_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |   BOLT-LMM, v2.3.<span class="idiff left right">5</span>   /_ /   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

58

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<td class="new_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |   <span class="idiff left">March</span> 2<span class="idiff">0</span>, 2021    <span class="idiff right">  </span>/_/   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |   BOLT-LMM, v2.3.<span class="idiff left right">6</span>   /_ /   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |   <span class="idiff left">October</span> 2<span class="idiff right">9</span>, 2021    /_/   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |   Po-Ru Loh            //   |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      |                        /    |"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"                      +-----------------------------+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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