@----------------------------------------------------------@
|        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 [ /data/Pernilla/Plink_output/QTLs0.log ]
Analysis started: Wed Sep 19 16:14:01 2012

Options in effect:
	--ped /data/Pernilla/new_ped.txt
	--map /data/Pernilla/map_w_X.txt
	--noweb
	--no-pheno
	--compound-genotypes
	--map3
	--missing-genotype N
	--out /data/Pernilla/Plink_output/QTLs0

265551 (of 265551) markers to be included from [ /data/Pernilla/map_w_X.txt ]
1407 individuals read from [ /data/Pernilla/new_ped.txt ] 
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 1407 missing
748 males, 659 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 265551 SNPs
0 founders and 1407 non-founders found
2123 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ /data/Pernilla/Plink_output/QTLs0.hh ]
265551 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ /data/Pernilla/Plink_output/QTLs0.nof ]
Total genotyping rate in remaining individuals is 0.998954
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 265551 SNPs
After filtering, 0 cases, 0 controls and 1407 missing
After filtering, 748 males, 659 females, and 0 of unspecified sex

Analysis finished: Wed Sep 19 16:17:37 2012