@----------------------------------------------------------@
|        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 [ balkan_geno003.log ]
Analysis started: Wed Jan 21 20:45:37 2015

Options in effect:
	--bfile /ebc_data/chipdata/Master_data/Master_Data
	--noweb
	--keep balkan.ind
	--geno 0.03
	--make-bed
	--out balkan_geno003

Reading map (extended format) from [ /ebc_data/chipdata/Master_data/Master_Data.bim ] 
1282568 markers to be included from [ /ebc_data/chipdata/Master_data/Master_Data.bim ]
Reading pedigree information from [ /ebc_data/chipdata/Master_data/Master_Data.fam ] 
4749 individuals read from [ /ebc_data/chipdata/Master_data/Master_Data.fam ] 
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 4749 missing
3209 males, 1458 females, and 82 of unspecified sex
Warning, found 82 individuals with ambiguous sex codes
Writing list of these individuals to [ balkan_geno003.nosex ]
Reading genotype bitfile from [ /ebc_data/chipdata/Master_data/Master_Data.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Reading individuals to keep [ balkan.ind ] ... 70 read
4679 individuals removed with --keep option
Before frequency and genotyping pruning, there are 1282568 SNPs
70 founders and 0 non-founders found
20 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ balkan_geno003.hh ]
Total genotyping rate in remaining individuals is 0.433992
727321 SNPs failed missingness test ( GENO > 0.03 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 555247 SNPs
After filtering, 0 cases, 0 controls and 70 missing
After filtering, 31 males, 39 females, and 0 of unspecified sex
Writing pedigree information to [ balkan_geno003.fam ] 
Writing map (extended format) information to [ balkan_geno003.bim ] 
Writing genotype bitfile to [ balkan_geno003.bed ] 
Using (default) SNP-major mode

Analysis finished: Wed Jan 21 20:50:28 2015