/test-data/rgCaCotest1_CaCo_log.txt
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1 2@----------------------------------------------------------@ 3| PLINK! | v1.07 | 10/Aug/2009 | 4|----------------------------------------------------------| 5| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 6|----------------------------------------------------------| 7| For documentation, citation & bug-report instructions: | 8| http://pngu.mgh.harvard.edu/purcell/plink/ | 9@----------------------------------------------------------@ 10 11Skipping web check... [ --noweb ] 12Writing this text to log file [ rgCaCotest1.log ] 13Analysis started: Sun May 9 21:23:49 2010 14 15Options in effect: 16 --noweb 17 --bfile /share/shared/galaxy/test-data/tinywga 18 --out rgCaCotest1 19 --model 20 21Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 2225 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] 23Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 2440 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 2540 individuals with nonmissing phenotypes 26Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 27Missing phenotype value is also -9 2810 cases, 30 controls and 0 missing 2921 males, 19 females, and 0 of unspecified sex 30Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 31Detected that binary PED file is v1.00 SNP-major mode 32Before frequency and genotyping pruning, there are 25 SNPs 3327 founders and 13 non-founders found 34Total genotyping rate in remaining individuals is 0.995 350 SNPs failed missingness test ( GENO > 1 ) 360 SNPs failed frequency test ( MAF < 0 ) 37After frequency and genotyping pruning, there are 25 SNPs 38After filtering, 10 cases, 30 controls and 0 missing 39After filtering, 21 males, 19 females, and 0 of unspecified sex 40Full-model association tests, minimum genotype count: --cell 5 41Writing full model association results to [ rgCaCotest1.model ] 42 43Analysis finished: Sun May 9 21:23:49 2010 44 45###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 46Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49