/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log
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1## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 2## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner 3## 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 4 5@----------------------------------------------------------@ 6| PLINK! | v1.07 | 10/Aug/2009 | 7|----------------------------------------------------------| 8| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 9|----------------------------------------------------------| 10| For documentation, citation & bug-report instructions: | 11| http://pngu.mgh.harvard.edu/purcell/plink/ | 12@----------------------------------------------------------@ 13 14Skipping web check... [ --noweb ] 15Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] 16Analysis started: Sun May 9 21:23:42 2010 17 18Options in effect: 19 --noweb 20 --bfile /share/shared/galaxy/test-data/tinywga 21 --indep-pairwise 10000 5000 0.1 22 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 23 --mind 1 24 --geno 1 25 --maf 0 26 --hwe 0 27 --me 1 1 28 29Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 3025 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] 31Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 3240 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 3340 individuals with nonmissing phenotypes 34Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 35Missing phenotype value is also -9 3610 cases, 30 controls and 0 missing 3721 males, 19 females, and 0 of unspecified sex 38Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 39Detected that binary PED file is v1.00 SNP-major mode 40Before frequency and genotyping pruning, there are 25 SNPs 4127 founders and 13 non-founders found 420 markers to be excluded based on HWE test ( p <= 0 ) 43 0 markers failed HWE test in cases 44 0 markers failed HWE test in controls 45Total genotyping rate in remaining individuals is 0.995 460 SNPs failed missingness test ( GENO > 1 ) 470 SNPs failed frequency test ( MAF < 0 ) 48After frequency and genotyping pruning, there are 25 SNPs 49After filtering, 10 cases, 30 controls and 0 missing 50After filtering, 21 males, 19 females, and 0 of unspecified sex 5114 nuclear families, 1 founder singletons found 5213 non-founders with 2 parents in 13 nuclear families 530 non-founders without 2 parents in 0 nuclear families 5410 affected offspring trios 550 phenotypically discordant parent pairs found 56Converting data to Individual-major format 57Filtering SNPs/families for Mendel Error rates above 1, 1 580 Mendel errors detected in total 590 families ( 0 individuals ) removed due to Mendel errors 600 markers removed due to Mendel errors, 25 remaining 61Converting data to SNP-major format 62Performing LD-based pruning... 63Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] 64Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] 65Scanning from chromosome 22 to 22 66 67Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] 68For chromosome 22, 22 SNPs pruned out, 3 remaining 69 70Analysis finished: Sun May 9 21:23:42 2010 71 72 73## 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 74 75@----------------------------------------------------------@ 76| PLINK! | v1.07 | 10/Aug/2009 | 77|----------------------------------------------------------| 78| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 79|----------------------------------------------------------| 80| For documentation, citation & bug-report instructions: | 81| http://pngu.mgh.harvard.edu/purcell/plink/ | 82@----------------------------------------------------------@ 83 84Skipping web check... [ --noweb ] 85Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] 86Analysis started: Sun May 9 21:23:42 2010 87 88Options in effect: 89 --noweb 90 --bfile /share/shared/galaxy/test-data/tinywga 91 --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in 92 --make-bed 93 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 94 95Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 9625 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] 97Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 9840 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 9940 individuals with nonmissing phenotypes 100Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 101Missing phenotype value is also -9 10210 cases, 30 controls and 0 missing 10321 males, 19 females, and 0 of unspecified sex 104Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 105Detected that binary PED file is v1.00 SNP-major mode 106Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read 107Before frequency and genotyping pruning, there are 3 SNPs 10827 founders and 13 non-founders found 109Total genotyping rate in remaining individuals is 1 1100 SNPs failed missingness test ( GENO > 1 ) 1110 SNPs failed frequency test ( MAF < 0 ) 112After frequency and genotyping pruning, there are 3 SNPs 113After filtering, 10 cases, 30 controls and 0 missing 114After filtering, 21 males, 19 females, and 0 of unspecified sex 115Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 116Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 117Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 118Using (default) SNP-major mode 119 120Analysis finished: Sun May 9 21:23:42 2010 121 122 123## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 124 125@----------------------------------------------------------@ 126| PLINK! | v1.07 | 10/Aug/2009 | 127|----------------------------------------------------------| 128| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 129|----------------------------------------------------------| 130| For documentation, citation & bug-report instructions: | 131| http://pngu.mgh.harvard.edu/purcell/plink/ | 132@----------------------------------------------------------@ 133 134Skipping web check... [ --noweb ] 135Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] 136Analysis started: Sun May 9 21:23:42 2010 137 138Options in effect: 139 --noweb 140 --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 141 --recode 142 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 143 144Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 1453 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 146Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 14740 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 14840 individuals with nonmissing phenotypes 149Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 150Missing phenotype value is also -9 15110 cases, 30 controls and 0 missing 15221 males, 19 females, and 0 of unspecified sex 153Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 154Detected that binary PED file is v1.00 SNP-major mode 155Before frequency and genotyping pruning, there are 3 SNPs 15627 founders and 13 non-founders found 157Total genotyping rate in remaining individuals is 1 1580 SNPs failed missingness test ( GENO > 1 ) 1590 SNPs failed frequency test ( MAF < 0 ) 160After frequency and genotyping pruning, there are 3 SNPs 161After filtering, 10 cases, 30 controls and 0 missing 162After filtering, 21 males, 19 females, and 0 of unspecified sex 163Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] 164Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] 165 166Analysis finished: Sun May 9 21:23:42 2010 167 168 169