/test-data/rgGLMtest1_GLM_log.txt

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  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']
    2. 

  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
    4. 

  4. ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127
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  5. 

  6. 

  7. @----------------------------------------------------------@
    8. 

  8. |        PLINK!       |     v1.07      |   10/Aug/2009     |
    9. 

  9. |----------------------------------------------------------|
    10. 

  10. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    11. 

  11. |----------------------------------------------------------|
    12. 

  12. |  For documentation, citation & bug-report instructions:  |
    13. 

  13. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    14. 

  14. @----------------------------------------------------------@
    15. 

  15. 

  16. Skipping web check... [ --noweb ] 
    17. 

  17. Writing this text to log file [ tinywga.log ]
    18. 

  18. Analysis started: Sun May  9 21:23:49 2010
    19. 

  19. 

  20. Options in effect:
    21. 

  21. 	--noweb
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  22. 	--bfile /share/shared/galaxy/test-data/tinywga
    23. 

  23. 	--pheno-name c1
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  24. 	--pheno /share/shared/galaxy/test-data/tinywga.pphe
    25. 

  25. 	--out tinywga
    26. 

  26. 	--mind 1
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  27. 	--geno 1
    28. 

  28. 	--maf 0
    29. 

  29. 	--linear
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  30. 

  31. Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
    32. 

  32. 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
    33. 

  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 ] 
    35. 

  35. 40 individuals with nonmissing phenotypes
    36. 

  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. 

  57. Analysis finished: Sun May  9 21:23:49 2010
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