## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 @----------------------------------------------------------@ | 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 [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 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 0 markers to be excluded based on HWE test ( p <= 0 ) 0 markers failed HWE test in cases 0 markers failed HWE test in controls 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 14 nuclear families, 1 founder singletons found 13 non-founders with 2 parents in 13 nuclear families 0 non-founders without 2 parents in 0 nuclear families 10 affected offspring trios 0 phenotypically discordant parent pairs found Converting data to Individual-major format Filtering SNPs/families for Mendel Error rates above 1, 1 0 Mendel errors detected in total 0 families ( 0 individuals ) removed due to Mendel errors 0 markers removed due to Mendel errors, 25 remaining Converting data to SNP-major format Performing LD-based pruning... Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] Scanning from chromosome 22 to 22 Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] For chromosome 22, 22 SNPs pruned out, 3 remaining Analysis finished: Sun May 9 21:23:42 2010 ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ | 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 [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 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 Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 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 [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Using (default) SNP-major mode Analysis finished: Sun May 9 21:23:42 2010 ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ | 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 [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.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/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] Analysis finished: Sun May 9 21:23:42 2010