| 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 | |
|---|
| 14 | Skipping web check... [ --noweb ] |
|---|
| 15 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
|---|
| 16 | Analysis started: Sun May 9 21:23:42 2010 |
|---|
| 17 | |
|---|
| 18 | Options 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 | |
|---|
| 29 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
|---|
| 30 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
|---|
| 31 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
|---|
| 32 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
|---|
| 33 | 40 individuals with nonmissing phenotypes |
|---|
| 34 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
|---|
| 35 | Missing phenotype value is also -9 |
|---|
| 36 | 10 cases, 30 controls and 0 missing |
|---|
| 37 | 21 males, 19 females, and 0 of unspecified sex |
|---|
| 38 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
|---|
| 39 | Detected that binary PED file is v1.00 SNP-major mode |
|---|
| 40 | Before frequency and genotyping pruning, there are 25 SNPs |
|---|
| 41 | 27 founders and 13 non-founders found |
|---|
| 42 | 0 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 |
|---|
| 45 | Total genotyping rate in remaining individuals is 0.995 |
|---|
| 46 | 0 SNPs failed missingness test ( GENO > 1 ) |
|---|
| 47 | 0 SNPs failed frequency test ( MAF < 0 ) |
|---|
| 48 | After frequency and genotyping pruning, there are 25 SNPs |
|---|
| 49 | After filtering, 10 cases, 30 controls and 0 missing |
|---|
| 50 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
|---|
| 51 | 14 nuclear families, 1 founder singletons found |
|---|
| 52 | 13 non-founders with 2 parents in 13 nuclear families |
|---|
| 53 | 0 non-founders without 2 parents in 0 nuclear families |
|---|
| 54 | 10 affected offspring trios |
|---|
| 55 | 0 phenotypically discordant parent pairs found |
|---|
| 56 | Converting data to Individual-major format |
|---|
| 57 | Filtering SNPs/families for Mendel Error rates above 1, 1 |
|---|
| 58 | 0 Mendel errors detected in total |
|---|
| 59 | 0 families ( 0 individuals ) removed due to Mendel errors |
|---|
| 60 | 0 markers removed due to Mendel errors, 25 remaining |
|---|
| 61 | Converting data to SNP-major format |
|---|
| 62 | Performing LD-based pruning... |
|---|
| 63 | Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] |
|---|
| 64 | Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] |
|---|
| 65 | Scanning from chromosome 22 to 22 |
|---|
| 66 | |
|---|
| 67 | Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] |
|---|
| 68 | For chromosome 22, 22 SNPs pruned out, 3 remaining |
|---|
| 69 | |
|---|
| 70 | Analysis 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 | |
|---|
| 84 | Skipping web check... [ --noweb ] |
|---|
| 85 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
|---|
| 86 | Analysis started: Sun May 9 21:23:42 2010 |
|---|
| 87 | |
|---|
| 88 | Options 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 | |
|---|
| 95 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
|---|
| 96 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
|---|
| 97 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
|---|
| 98 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
|---|
| 99 | 40 individuals with nonmissing phenotypes |
|---|
| 100 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
|---|
| 101 | Missing phenotype value is also -9 |
|---|
| 102 | 10 cases, 30 controls and 0 missing |
|---|
| 103 | 21 males, 19 females, and 0 of unspecified sex |
|---|
| 104 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
|---|
| 105 | Detected that binary PED file is v1.00 SNP-major mode |
|---|
| 106 | Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read |
|---|
| 107 | Before frequency and genotyping pruning, there are 3 SNPs |
|---|
| 108 | 27 founders and 13 non-founders found |
|---|
| 109 | Total genotyping rate in remaining individuals is 1 |
|---|
| 110 | 0 SNPs failed missingness test ( GENO > 1 ) |
|---|
| 111 | 0 SNPs failed frequency test ( MAF < 0 ) |
|---|
| 112 | After frequency and genotyping pruning, there are 3 SNPs |
|---|
| 113 | After filtering, 10 cases, 30 controls and 0 missing |
|---|
| 114 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
|---|
| 115 | Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
|---|
| 116 | Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
|---|
| 117 | Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] |
|---|
| 118 | Using (default) SNP-major mode |
|---|
| 119 | |
|---|
| 120 | Analysis 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 | |
|---|
| 134 | Skipping web check... [ --noweb ] |
|---|
| 135 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] |
|---|
| 136 | Analysis started: Sun May 9 21:23:42 2010 |
|---|
| 137 | |
|---|
| 138 | Options 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 | |
|---|
| 144 | Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
|---|
| 145 | 3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] |
|---|
| 146 | Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
|---|
| 147 | 40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] |
|---|
| 148 | 40 individuals with nonmissing phenotypes |
|---|
| 149 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
|---|
| 150 | Missing phenotype value is also -9 |
|---|
| 151 | 10 cases, 30 controls and 0 missing |
|---|
| 152 | 21 males, 19 females, and 0 of unspecified sex |
|---|
| 153 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] |
|---|
| 154 | Detected that binary PED file is v1.00 SNP-major mode |
|---|
| 155 | Before frequency and genotyping pruning, there are 3 SNPs |
|---|
| 156 | 27 founders and 13 non-founders found |
|---|
| 157 | Total genotyping rate in remaining individuals is 1 |
|---|
| 158 | 0 SNPs failed missingness test ( GENO > 1 ) |
|---|
| 159 | 0 SNPs failed frequency test ( MAF < 0 ) |
|---|
| 160 | After frequency and genotyping pruning, there are 3 SNPs |
|---|
| 161 | After filtering, 10 cases, 30 controls and 0 missing |
|---|
| 162 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
|---|
| 163 | Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] |
|---|
| 164 | Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] |
|---|
| 165 | |
|---|
| 166 | Analysis finished: Sun May 9 21:23:42 2010 |
|---|
| 167 | |
|---|
| 168 | |
|---|
| 169 | |
|---|
![(trac.ini の [header_logo] セクションを設定してください)](/bh10.10/chrome/site/your_project_logo.png){kind=logo}
