[2] | 1 | rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff'] |
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| 2 | vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] |
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| 3 | xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls |
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| 4 | ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 |
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| 5 | |
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| 6 | |
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| 7 | @----------------------------------------------------------@ |
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| 8 | | PLINK! | v1.07 | 10/Aug/2009 | |
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| 9 | |----------------------------------------------------------| |
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| 10 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 11 | |----------------------------------------------------------| |
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| 12 | | For documentation, citation & bug-report instructions: | |
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| 13 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 14 | @----------------------------------------------------------@ |
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| 15 | |
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| 16 | Skipping web check... [ --noweb ] |
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| 17 | Writing this text to log file [ tinywga.log ] |
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| 18 | Analysis started: Sun May 9 21:23:49 2010 |
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| 19 | |
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| 20 | Options in effect: |
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| 21 | --noweb |
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| 22 | --bfile /share/shared/galaxy/test-data/tinywga |
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| 23 | --pheno-name c1 |
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| 24 | --pheno /share/shared/galaxy/test-data/tinywga.pphe |
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| 25 | --out tinywga |
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| 26 | --mind 1 |
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| 27 | --geno 1 |
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| 28 | --maf 0 |
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| 29 | --linear |
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| 30 | |
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| 31 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 32 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 33 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 34 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 35 | 40 individuals with nonmissing phenotypes |
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| 36 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 37 | Missing phenotype value is also -9 |
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| 38 | 10 cases, 30 controls and 0 missing |
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| 39 | 21 males, 19 females, and 0 of unspecified sex |
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| 40 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
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| 41 | Detected that binary PED file is v1.00 SNP-major mode |
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| 42 | Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] |
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| 43 | 40 individuals with non-missing alternate phenotype |
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| 44 | Assuming a quantitative trait |
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| 45 | Missing phenotype value is -9 |
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| 46 | Before frequency and genotyping pruning, there are 25 SNPs |
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| 47 | 27 founders and 13 non-founders found |
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| 48 | Total genotyping rate in remaining individuals is 0.995 |
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| 49 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 50 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 51 | After frequency and genotyping pruning, there are 25 SNPs |
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| 52 | After filtering, 40 individuals with non-missing status |
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| 53 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 54 | Converting data to Individual-major format |
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| 55 | Writing linear model association results to [ tinywga.assoc.linear ] |
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| 56 | |
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| 57 | Analysis finished: Sun May 9 21:23:49 2010 |
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| 58 | |
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