@----------------------------------------------------------@ | 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 [ /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.log ] Analysis started: Fri Mar 27 10:00:10 2015 Options in effect: --noweb --tfile Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians --make-bed --out /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians Reading pedigree information from [ Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.tfam ] 452 individuals read from [ Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.tfam ] 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 452 missing 0 males, 0 females, and 452 of unspecified sex Warning, found 452 individuals with ambiguous sex codes Writing list of these individuals to [ /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.nosex ] 35557 (of 35557) markers to be included from [ Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.tped ] Before frequency and genotyping pruning, there are 35557 SNPs 452 founders and 0 non-founders found Total genotyping rate in remaining individuals is nan 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 35557 SNPs After filtering, 0 cases, 0 controls and 452 missing After filtering, 0 males, 0 females, and 452 of unspecified sex Writing pedigree information to [ /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.fam ] Writing map (extended format) information to [ /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.bim ] Writing genotype bitfile to [ /ebc_data/web/chrY/PLINKandVCF/Karmin_et_al_2015_chrY_452samples_CGonly_filtered1_noAustralians.bed ] Using (default) SNP-major mode Analysis finished: Fri Mar 27 10:00:18 2015