@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/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 [ /Net/mus/data/HSrats/rats/genome_cache_oct/MAFs/MAFs.log ]
Analysis started: Mon Apr 23 19:46:12 2012

Options in effect:
	--noweb
	--ped /Net/mus/data/HSrats/rats/genome_cache_oct/ped4pedCheck.txt
	--map /Net/mus/data/HSrats/rats/genome_cache_oct/map4pedCheck.txt
	--nonfounders
	--compound-genotypes
	--map3
	--missing-genotype N
	--no-pheno
	--allow-no-sex
	--freq
	--out /Net/mus/data/HSrats/rats/genome_cache_oct/MAFs/MAFs

261684 (of 261684) markers to be included from [ /Net/mus/data/HSrats/rats/genome_cache_oct/map4pedCheck.txt ]
Warning, found 1407 individuals with ambiguous sex codes
Writing list of these individuals to [ /Net/mus/data/HSrats/rats/genome_cache_oct/MAFs/MAFs.nosex ]
1603 individuals read from [ /Net/mus/data/HSrats/rats/genome_cache_oct/ped4pedCheck.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 1603 missing
96 males, 100 females, and 1407 of unspecified sex
Before frequency and genotyping pruning, there are 261684 SNPs
0 founders and 1603 non-founders found
Writing allele frequencies (all individuals) to [ /Net/mus/data/HSrats/rats/genome_cache_oct/MAFs/MAFs.frq ] 

Analysis finished: Mon Apr 23 19:57:53 2012