--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MDSplot/test-data/analyse.log	Thu Feb 26 16:09:14 2015 -0500
@@ -0,0 +1,56 @@
+
+@----------------------------------------------------------@
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
+|----------------------------------------------------------|
+|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
+|----------------------------------------------------------|
+|  For documentation, citation & bug-report instructions:  |
+|        http://pngu.mgh.harvard.edu/purcell/plink/        |
+@----------------------------------------------------------@
+
+Skipping web check... [ --noweb ] 
+Writing this text to log file [ analyse.log ]
+Analysis started: Tue Jan 20 09:30:56 2015
+
+Options in effect:
+	--file input
+	--noweb
+	--cluster
+	--matrix
+	--mds-plot 2
+	--out analyse
+
+2013 (of 2013) markers to be included from [ input.map ]
+93 individuals read from [ input.ped ] 
+93 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+0 cases, 93 controls and 0 missing
+93 males, 0 females, and 0 of unspecified sex
+Before frequency and genotyping pruning, there are 2013 SNPs
+Converting data to SNP-major format
+93 founders and 0 non-founders found
+Total genotyping rate in remaining individuals is 1
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+Converting data to Individual-major format
+After frequency and genotyping pruning, there are 2013 SNPs
+After filtering, 0 cases, 93 controls and 0 missing
+After filtering, 93 males, 0 females, and 0 of unspecified sex
+
+ **Warning** this analysis typically requires whole-genome level data
+             to give accurate results 
+
+Clustering individuals based on genome-wide IBS
+Merge distance p-value constraint = 0
+IBS(g) calculation: 0 of 4278         
IBS(g) calculation: 100 of 4278         
IBS(g) calculation: 200 of 4278         
IBS(g) calculation: 300 of 4278         
IBS(g) calculation: 400 of 4278         
IBS(g) calculation: 500 of 4278         
IBS(g) calculation: 600 of 4278         
IBS(g) calculation: 700 of 4278         
IBS(g) calculation: 800 of 4278         
IBS(g) calculation: 900 of 4278         
IBS(g) calculation: 1000 of 4278         
IBS(g) calculation: 1100 of 4278         
IBS(g) calculation: 1200 of 4278         
IBS(g) calculation: 1300 of 4278         
IBS(g) calculation: 1400 of 4278         
IBS(g) calculation: 1500 of 4278         
IBS(g) calculation: 1600 of 4278         
IBS(g) calculation: 1700 of 4278         
IBS(g) calculation: 1800 of 4278         
IBS(g) calculation: 1900 of 4278         
IBS(g) calculation: 2000 of 4278         
IBS(g) calculation: 2100 of 4278         
IBS(g) calculation: 2200 of 4278         
IBS(g) calculation: 2300 of 4278         
IBS(g) calculation: 2400 of 4278         
IBS(g) calculation: 2500 of 4278         
IBS(g) calculation: 2600 of 4278         
IBS(g) calculation: 2700 of 4278         
IBS(g) calculation: 2800 of 4278         
IBS(g) calculation: 2900 of 4278         
IBS(g) calculation: 3000 of 4278         
IBS(g) calculation: 3100 of 4278         
IBS(g) calculation: 3200 of 4278         
IBS(g) calculation: 3300 of 4278         
IBS(g) calculation: 3400 of 4278         
IBS(g) calculation: 3500 of 4278         
IBS(g) calculation: 3600 of 4278         
IBS(g) calculation: 3700 of 4278         
IBS(g) calculation: 3800 of 4278         
IBS(g) calculation: 3900 of 4278         
IBS(g) calculation: 4000 of 4278         
IBS(g) calculation: 4100 of 4278         
IBS(g) calculation: 4200 of 4278         
Writing IBS similarity matrix to [ analyse.mibs ]
+Of these, 4278 are pairable based on constraints
+Writing cluster progress to [ analyse.cluster0 ]
+Writing cluster solution (1) [ analyse.cluster1 ]
+Writing cluster solution (2) [ analyse.cluster2 ]
+Writing cluster solution (3) [ analyse.cluster3 ]
+Writing MDS solution to [ analyse.mds ] 
+MDS plot of individuals (not clusters)
+
+Analysis finished: Tue Jan 20 09:30:57 2015
+