<div dir="ltr">Hi I am trying to create a strata for running an AMOVA. I am using a Genlight object but for some reason I am having the error below.<div> Can somebody help me, please? <br><div><br></div><div><br></div><div><pre tabindex="0" aria-label="Console Output" role="document" class="gmail-GNVWDDMDN3B" id="gmail-rstudio_console_output" style="font-family:Consolas,monospace;font-size:13.3333px;outline:none;border:none;word-break:break-all;margin-top:0px;margin-bottom:0px;line-height:1.2;color:rgb(255,255,255);background-color:rgb(0,34,64)"><span tabindex="-1" class="gmail-GNVWDDMDO3B" role="document" style="outline:none"><span class="gmail-GNVWDDMDE4B gmail-ace_keyword" style="color:rgb(255,157,0)">> </span><span class="gmail-GNVWDDMDD3B gmail-ace_keyword" style="color:rgb(255,157,0)">strata(gl) <- data.frame(other(gl))
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting gl.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting utils.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Topskip not provided.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Setting topskip to 6 .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Reading in the SNP data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Detected 2 row format.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Number of rows per clone (should be only  2 s): 2 </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added the following locus metrics:</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">AlleleID CloneID AlleleSequence TrimmedSequence SNP SnpPosition CallRate OneRatioRef OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RepAvg .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor4" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(150,203,254)">Recognised: 479 individuals and 76246  SNPs in a 2 row format using Report_DTu24-9051_2_moreOrders_SNP_1.csv </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: utils.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting utils.dart2genlight </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting conversion....</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Format is 2 rows.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Please note conversion of bigger data sets will take some time!</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Once finished, we recommend to save the object using save(object, file="object.rdata")</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Adding individual metrics: meta2.csv .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Ids for individual metadata (at least a subset of) are matching!</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Found  479 matching ids out of 479 ids provided in the ind.metadata file.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Added population assignments.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Added latlon data.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  id  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  pop  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  lat  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  lon  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: utils.dart2genlight </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">   479 rows and 76246 columns of data read</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Read depth calculated and added to the locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Minor Allele Frequency (MAF) calculated and added to the locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Recalculating locus metrics provided by DArT (optionally specified)</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting gl.compliance.check </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Processing genlight object with SNP data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking coding of SNPs</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    SNP data scored NA, 0, 1 or 2 confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for population assignments</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    Population assignments confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking locus metrics and flags</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Recalculating locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for monomorphic loci</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    No monomorphic loci detected</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for loci with all missing data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    No loci with all missing data detected</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking whether individual names are unique.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for individual metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    Individual metrics confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Spelling of coordinates checked and changed if necessary to </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">            lat/lon</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: gl.compliance.check </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: gl.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDH3B gmail-ace_constant gmail-ace_language" style="color:rgb(255,98,140)">Error in utils.check.datatype(x, verbose = verbose) : 
  </span><span class="gmail-GNVWDDMDH3B gmail-ace_constant gmail-ace_language gmail-xtermColor1" style="color:rgb(255,108,96)">Fatal Error: inappropriate object passed to function, found list expecting genlight or SNP or SilicoDArT</span><span class="gmail-GNVWDDMDH3B gmail-ace_constant gmail-ace_language" style="color:rgb(255,98,140)">
</span></span><span tabindex="-1" class="gmail-GNVWDDMDO3B" role="document" style="outline:none"><span class="gmail-GNVWDDMDE4B gmail-ace_keyword" style="color:rgb(255,157,0)">> </span><span class="gmail-GNVWDDMDD3B gmail-ace_keyword" style="color:rgb(255,157,0)">strata(gi) <- data.frame(other(gi))
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting gl.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting utils.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Topskip not provided.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Setting topskip to 6 .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Reading in the SNP data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Detected 2 row format.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Number of rows per clone (should be only  2 s): 2 </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added the following locus metrics:</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">AlleleID CloneID AlleleSequence TrimmedSequence SNP SnpPosition CallRate OneRatioRef OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RepAvg .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor4" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(150,203,254)">Recognised: 479 individuals and 76246  SNPs in a 2 row format using Report_DTu24-9051_2_moreOrders_SNP_1.csv </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: utils.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting utils.dart2genlight </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting conversion....</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Format is 2 rows.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Please note conversion of bigger data sets will take some time!</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Once finished, we recommend to save the object using save(object, file="object.rdata")</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Adding individual metrics: meta2.csv .</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Ids for individual metadata (at least a subset of) are matching!</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Found  479 matching ids out of 479 ids provided in the ind.metadata file.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Added population assignments.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Added latlon data.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  id  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  pop  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  lat  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
 </span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)"> Added  lon  to the other$ind.metrics slot.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: utils.dart2genlight </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">   479 rows and 76246 columns of data read</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Read depth calculated and added to the locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Minor Allele Frequency (MAF) calculated and added to the locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Recalculating locus metrics provided by DArT (optionally specified)</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Starting gl.compliance.check </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Processing genlight object with SNP data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking coding of SNPs</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    SNP data scored NA, 0, 1 or 2 confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for population assignments</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    Population assignments confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking locus metrics and flags</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Recalculating locus metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for monomorphic loci</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    No monomorphic loci detected</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for loci with all missing data</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    No loci with all missing data detected</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking whether individual names are unique.</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Checking for individual metrics</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">    Individual metrics confirmed</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">  Spelling of coordinates checked and changed if necessary to </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">            lat/lon</span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: gl.compliance.check </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDN3B gmail-xtermColor2" style="outline:none;border:none;word-break:break-all;margin:0px;color:rgb(168,255,96)">Completed: gl.read.dart </span><span class="gmail-GNVWDDMDN3B" style="outline:none;border:none;word-break:break-all;margin:0px">
</span><span class="gmail-GNVWDDMDH3B gmail-ace_constant gmail-ace_language" style="color:rgb(255,98,140)">Error in utils.check.datatype(x, verbose = verbose) : 
  </span><span class="gmail-GNVWDDMDH3B gmail-ace_constant gmail-ace_language gmail-xtermColor1" style="color:rgb(255,108,96)">Fatal Error: inappropriate object passed to function, found list expecting genlight or SNP or SilicoDArT</span></span></pre></div></div></div>