[2] | 1 | ## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 |
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| 2 | ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner |
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| 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 |
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| 4 | |
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| 5 | @----------------------------------------------------------@ |
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| 6 | | PLINK! | v1.07 | 10/Aug/2009 | |
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| 7 | |----------------------------------------------------------| |
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| 8 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 9 | |----------------------------------------------------------| |
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| 10 | | For documentation, citation & bug-report instructions: | |
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| 11 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 12 | @----------------------------------------------------------@ |
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| 13 | |
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| 14 | Skipping web check... [ --noweb ] |
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| 15 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
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| 16 | Analysis started: Sun May 9 21:23:42 2010 |
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| 17 | |
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| 18 | Options in effect: |
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| 19 | --noweb |
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| 20 | --bfile /share/shared/galaxy/test-data/tinywga |
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| 21 | --indep-pairwise 10000 5000 0.1 |
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| 22 | --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 |
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| 23 | --mind 1 |
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| 24 | --geno 1 |
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| 25 | --maf 0 |
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| 26 | --hwe 0 |
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| 27 | --me 1 1 |
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| 28 | |
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| 29 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 30 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 31 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 32 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 33 | 40 individuals with nonmissing phenotypes |
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| 34 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 35 | Missing phenotype value is also -9 |
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| 36 | 10 cases, 30 controls and 0 missing |
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| 37 | 21 males, 19 females, and 0 of unspecified sex |
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| 38 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
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| 39 | Detected that binary PED file is v1.00 SNP-major mode |
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| 40 | Before frequency and genotyping pruning, there are 25 SNPs |
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| 41 | 27 founders and 13 non-founders found |
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| 42 | 0 markers to be excluded based on HWE test ( p <= 0 ) |
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| 43 | 0 markers failed HWE test in cases |
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| 44 | 0 markers failed HWE test in controls |
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| 45 | Total genotyping rate in remaining individuals is 0.995 |
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| 46 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 47 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 48 | After frequency and genotyping pruning, there are 25 SNPs |
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| 49 | After filtering, 10 cases, 30 controls and 0 missing |
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| 50 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 51 | 14 nuclear families, 1 founder singletons found |
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| 52 | 13 non-founders with 2 parents in 13 nuclear families |
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| 53 | 0 non-founders without 2 parents in 0 nuclear families |
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| 54 | 10 affected offspring trios |
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| 55 | 0 phenotypically discordant parent pairs found |
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| 56 | Converting data to Individual-major format |
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| 57 | Filtering SNPs/families for Mendel Error rates above 1, 1 |
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| 58 | 0 Mendel errors detected in total |
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| 59 | 0 families ( 0 individuals ) removed due to Mendel errors |
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| 60 | 0 markers removed due to Mendel errors, 25 remaining |
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| 61 | Converting data to SNP-major format |
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| 62 | Performing LD-based pruning... |
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| 63 | Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] |
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| 64 | Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] |
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| 65 | Scanning from chromosome 22 to 22 |
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| 66 | |
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| 67 | Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] |
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| 68 | For chromosome 22, 22 SNPs pruned out, 3 remaining |
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| 69 | |
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| 70 | Analysis finished: Sun May 9 21:23:42 2010 |
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| 71 | |
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| 72 | |
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| 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 |
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| 74 | |
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| 75 | @----------------------------------------------------------@ |
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| 76 | | PLINK! | v1.07 | 10/Aug/2009 | |
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| 77 | |----------------------------------------------------------| |
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| 78 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 79 | |----------------------------------------------------------| |
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| 80 | | For documentation, citation & bug-report instructions: | |
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| 81 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 82 | @----------------------------------------------------------@ |
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| 83 | |
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| 84 | Skipping web check... [ --noweb ] |
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| 85 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
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| 86 | Analysis started: Sun May 9 21:23:42 2010 |
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| 87 | |
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| 88 | Options in effect: |
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| 89 | --noweb |
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| 90 | --bfile /share/shared/galaxy/test-data/tinywga |
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| 91 | --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in |
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| 92 | --make-bed |
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| 93 | --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 |
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| 94 | |
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| 95 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 96 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 97 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 98 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 99 | 40 individuals with nonmissing phenotypes |
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| 100 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 101 | Missing phenotype value is also -9 |
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| 102 | 10 cases, 30 controls and 0 missing |
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| 103 | 21 males, 19 females, and 0 of unspecified sex |
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| 104 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
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| 105 | Detected that binary PED file is v1.00 SNP-major mode |
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| 106 | Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read |
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| 107 | Before frequency and genotyping pruning, there are 3 SNPs |
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| 108 | 27 founders and 13 non-founders found |
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| 109 | Total genotyping rate in remaining individuals is 1 |
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| 110 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 111 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 112 | After frequency and genotyping pruning, there are 3 SNPs |
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| 113 | After filtering, 10 cases, 30 controls and 0 missing |
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| 114 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 115 | Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
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| 116 | Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
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| 117 | Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] |
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| 118 | Using (default) SNP-major mode |
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| 119 | |
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| 120 | Analysis finished: Sun May 9 21:23:42 2010 |
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| 121 | |
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| 122 | |
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| 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 |
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| 124 | |
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| 125 | @----------------------------------------------------------@ |
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| 126 | | PLINK! | v1.07 | 10/Aug/2009 | |
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| 127 | |----------------------------------------------------------| |
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| 128 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 129 | |----------------------------------------------------------| |
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| 130 | | For documentation, citation & bug-report instructions: | |
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| 131 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 132 | @----------------------------------------------------------@ |
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| 133 | |
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| 134 | Skipping web check... [ --noweb ] |
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| 135 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
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| 136 | Analysis started: Sun May 9 21:23:42 2010 |
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| 137 | |
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| 138 | Options in effect: |
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| 139 | --noweb |
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| 140 | --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 |
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| 141 | --recode |
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| 142 | --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 |
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| 143 | |
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| 144 | Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
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| 145 | 3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
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| 146 | Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
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| 147 | 40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
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| 148 | 40 individuals with nonmissing phenotypes |
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| 149 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 150 | Missing phenotype value is also -9 |
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| 151 | 10 cases, 30 controls and 0 missing |
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| 152 | 21 males, 19 females, and 0 of unspecified sex |
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| 153 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] |
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| 154 | Detected that binary PED file is v1.00 SNP-major mode |
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| 155 | Before frequency and genotyping pruning, there are 3 SNPs |
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| 156 | 27 founders and 13 non-founders found |
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| 157 | Total genotyping rate in remaining individuals is 1 |
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| 158 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 159 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 160 | After frequency and genotyping pruning, there are 3 SNPs |
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| 161 | After filtering, 10 cases, 30 controls and 0 missing |
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| 162 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 163 | Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] |
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| 164 | Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] |
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| 165 | |
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| 166 | Analysis finished: Sun May 9 21:23:42 2010 |
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| 167 | |
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| 169 | |
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