@----------------------------------------------------------@
|        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/HSrats/rats/genome_cache_oct/MAFs_1407_non_X_260K/MAFs.log ]
Analysis started: Tue Aug 14 02:25:03 2012

Options in effect:
	--noweb
	--ped /data/HSrats/rats/genome_cache_oct/ped_w_X_w_founders_column.txt
	--keep /data/HSrats/rats/genome_cache_oct/cels_1407_w_founders_column.txt
	--map /data/HSrats/rats/genome_cache_oct/map_w_X.txt
	--nonfounders
	--compound-genotypes
	--map3
	--missing-genotype N
	--no-pheno
	--allow-no-sex
	--no-parents
	--no-sex
	--freq
	--out /data/HSrats/rats/genome_cache_oct/MAFs_1407_non_X_260K/MAFs
	--extract /data/HSrats/rats/genome_cache_oct/non_X_SNPs.txt

265551 (of 265551) markers to be included from [ /data/HSrats/rats/genome_cache_oct/map_w_X.txt ]
Warning, found 1610 individuals with ambiguous sex codes
Writing list of these individuals to [ /data/HSrats/rats/genome_cache_oct/MAFs_1407_non_X_260K/MAFs.nosex ]
1610 individuals read from [ /data/HSrats/rats/genome_cache_oct/ped_w_X_w_founders_column.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 1610 missing
0 males, 0 females, and 1610 of unspecified sex
Reading list of SNPs to extract [ /data/HSrats/rats/genome_cache_oct/non_X_SNPs.txt ] ... 261684 read
Reading individuals to keep [ /data/HSrats/rats/genome_cache_oct/cels_1407_w_founders_column.txt ] ... 1407 read
203 individuals removed with --keep option
Before frequency and genotyping pruning, there are 261684 SNPs
1407 founders and 0 non-founders found
Writing allele frequencies (all individuals) to [ /data/HSrats/rats/genome_cache_oct/MAFs_1407_non_X_260K/MAFs.frq ] 

Analysis finished: Tue Aug 14 02:28:40 2012