@----------------------------------------------------------@
|        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 [ ldp_tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
	--noweb
	--bfile /opt/galaxy/test-data/tinywga
	--extract tinywga.prune.in
	--make-bed
	--out ldp_tinywga

Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read
Before frequency and genotyping pruning, there are 14 SNPs
27 founders and 13 non-founders found
Total genotyping rate in remaining individuals is 0.991071
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 14 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
Writing pedigree information to [ ldp_tinywga.fam ] 
Writing map (extended format) information to [ ldp_tinywga.bim ] 
Writing genotype bitfile to [ ldp_tinywga.bed ] 
Using (default) SNP-major mode

Analysis finished: Wed May 19 15:15:38 2010