root/galaxy-central/test-data/rgCaCotest1_CaCo_log.txt

@----------------------------------------------------------@
|        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 [ rgCaCotest1.log ]
Analysis started: Sun May  9 21:23:49 2010

Options in effect:
        --noweb
        --bfile /share/shared/galaxy/test-data/tinywga
        --out rgCaCotest1
        --model

Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /share/shared/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 [ /share/shared/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
Full-model association tests, minimum genotype count: --cell 5
Writing full model association results to [ rgCaCotest1.model ] 

Analysis finished: Sun May  9 21:23:49 2010

###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772
Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49