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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