@----------------------------------------------------------@
|        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