/test-data/rgCaCotest1_CaCo_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 46 lines · 40 code · 6 blank · 0 comment · 0 complexity · 92cb93952c385ab25b25c42c797bc039 MD5 · raw file 

    

  1. @----------------------------------------------------------@
    2. 

  2. |        PLINK!       |     v1.07      |   10/Aug/2009     |
    3. 

  3. |----------------------------------------------------------|
    4. 

  4. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    5. 

  5. |----------------------------------------------------------|
    6. 

  6. |  For documentation, citation & bug-report instructions:  |
    7. 

  7. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    8. 

  8. @----------------------------------------------------------@
    9. 

  9. 

  10. Skipping web check... [ --noweb ] 
    11. 

  11. Writing this text to log file [ rgCaCotest1.log ]
    12. 

  12. Analysis started: Sun May  9 21:23:49 2010
    13. 

  13. 

  14. Options in effect:
    15. 

  15. 	--noweb
    16. 

  16. 	--bfile /share/shared/galaxy/test-data/tinywga
    17. 

  17. 	--out rgCaCotest1
    18. 

  18. 	--model
    19. 

  19. 

  20. Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
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  21. 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
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  22. Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
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  23. 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    24. 

  24. 40 individuals with nonmissing phenotypes
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  25. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
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  26. Missing phenotype value is also -9
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  27. 10 cases, 30 controls and 0 missing
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  28. 21 males, 19 females, and 0 of unspecified sex
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  29. Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
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  30. Detected that binary PED file is v1.00 SNP-major mode
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  31. Before frequency and genotyping pruning, there are 25 SNPs
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  32. 27 founders and 13 non-founders found
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  33. Total genotyping rate in remaining individuals is 0.995
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  34. 0 SNPs failed missingness test ( GENO > 1 )
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  35. 0 SNPs failed frequency test ( MAF < 0 )
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  36. After frequency and genotyping pruning, there are 25 SNPs
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  37. After filtering, 10 cases, 30 controls and 0 missing
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  38. After filtering, 21 males, 19 females, and 0 of unspecified sex
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  39. Full-model association tests, minimum genotype count: --cell 5
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  40. Writing full model association results to [ rgCaCotest1.model ] 
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  41. 

  42. Analysis finished: Sun May  9 21:23:49 2010
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  43. 

  44. ###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772
    45. 

  45. Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49
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