@----------------------------------------------------------@
|        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/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Recent cached web-check found... OK, v1.07 is current

Writing this text to log file [ dataSim40plink.log ]
Analysis started: Wed Feb 13 07:33:49 2013

Options in effect:
	--file dataSim40plink
	--indep 50 5 2
	--out dataSim40plink

10000 (of 10000) markers to be included from [ dataSim40plink.map ]
Warning, found 1000 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ dataSim40plink.nosex ]
1000 individuals read from [ dataSim40plink.ped ] 
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 1000 missing
0 males, 0 females, and 1000 of unspecified sex
Before frequency and genotyping pruning, there are 10000 SNPs
1000 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 )
After frequency and genotyping pruning, there are 10000 SNPs
After filtering, 0 cases, 0 controls and 1000 missing
After filtering, 0 males, 0 females, and 1000 of unspecified sex
Performing LD-based pruning...
Writing pruned-in SNPs to [ dataSim40plink.prune.in ]
Writing pruned-out SNPs to [ dataSim40plink.prune.out ]
Scanning from chromosome 1 to 1

Scan region on chromosome 1 from [ 1 ] to [ 10000 ]
For chromosome 1, 3353 SNPs pruned out, 6647 remaining

Analysis finished: Wed Feb 13 07:34:40 2013