<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Nevermind! </p>
<p>Finally got it to work on the mac, although the optimal K changed when assessing different ranges of K. </p>
<p>(Hopefully when I redo it with the original range of K I will get the same optimal K as I'm getting ready to publish!)</p>
<p><br>
</p>
<p>Cheers</p>
<p>Alan</p>
<br>
<div style="color: rgb(0, 0, 0);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org <adegenet-forum-bounces@lists.r-forge.r-project.org> on behalf of Alan Garcia-Elfring <alangarcia87@hotmail.com><br>
<b>Sent:</b> 01 October 2016 17:30<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] find.clusters() freezes on DAPC</font>
<div> </div>
</div>
<div>
<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi everyone,</p>
<p><br>
</p>
<p>I'm wondering if anyone has gotten stuck on the find.clusters function?</p>
<p><br>
</p>
<p>I did a DAPC on this exact dataset in some months back and now I want that I redo it to check a different K value and change the colours, but it keeps getting stuck on find.clusters. </p>
<p><br>
</p>
<p>Any idea what may be causing this? If I remember correctly, this step doesn't take long, definitely not more than a day.</p>
<p><br>
</p>
<p></p>
<div>
<div>I've tried on a new mac and also on a PC using<span style="font-family:Calibri,Arial,Helvetica,sans-serif,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"> the </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">parallel
= FALSE argument. </span></div>
<div><br>
</div>
<div>Any help is appreciated.</div>
<div><br>
</div>
<div>>pldata = read.PLINK("batch_1_recode.raw") <span style="font-family:Calibri,Arial,Helvetica,sans-serif,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"></span></div>
<div><br>
</div>
<div>>grp = find.clusters(pldata, max.n.clust = 15) ##GETS STUCK ON THIS</div>
<div><br>
</div>
<div><br>
</div>
<br>
</div>
<div><span style="font-size:12pt">/// GENLIGHT OBJECT /////////</span><br>
</div>
<div><br>
</div>
<div> // 229 genotypes, 62,236 binary SNPs, size: 15.3 Mb</div>
<div> </div>
<div><span style="font-size:12pt"> // Basic content</span><br>
</div>
<div> @gen: list of 229 SNPbin</div>
<div> @ploidy: ploidy of each individual (range: 2-2)</div>
<div><br>
</div>
<div> // Optional content</div>
<div> @ind.names: 229 individual labels</div>
<div> @loc.names: 62236 locus labels</div>
<div> @pop: population of each individual (group size range: 8-20)</div>
<div> @other: a list containing: sex phenotype pat mat </div>
<div><br>
</div>
<br>
<p></p>
<div id="Signature">
<div><b style="line-height:14.1999998092651px; color:rgb(0,0,128); font-family:Tahoma; font-size:x-small; background-color:rgb(255,255,255)"><font color="000000" face="Tahoma" style="line-height:normal"></font></b></div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>