@----------------------------------------------------------@
|        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 [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.log ]
Analysis started: Wed Jan  9 01:59:32 2013

Options in effect:
	--bfile /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH
	--noweb
	--keep jew.ind
	--geno 0.05
	--make-bed
	--out jew_paper_data_dbSNP-b131_pos-b37_1KG_strand

Reading map (extended format) from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bim ] 
1282089 markers to be included from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bim ]
Reading pedigree information from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.fam ] 
3828 individuals read from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.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 3828 missing
2648 males, 923 females, and 257 of unspecified sex
Warning, found 257 individuals with ambiguous sex codes
Writing list of these individuals to [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.nosex ]
Reading genotype bitfile from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Reading individuals to keep [ jew.ind ] ... 466 read
3362 individuals removed with --keep option
Before frequency and genotyping pruning, there are 1282089 SNPs
466 founders and 0 non-founders found
1236 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.hh ]
Total genotyping rate in remaining individuals is 0.451826
726352 SNPs failed missingness test ( GENO > 0.05 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 555737 SNPs
After filtering, 0 cases, 0 controls and 466 missing
After filtering, 378 males, 85 females, and 3 of unspecified sex
Writing pedigree information to [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.fam ] 
Writing map (extended format) information to [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.bim ] 
Writing genotype bitfile to [ jew_paper_data_dbSNP-b131_pos-b37_1KG_strand.bed ] 
Using (default) SNP-major mode

Analysis finished: Wed Jan  9 02:02:39 2013