/test-data/rgTDTtest1_TDT_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 53 lines · 47 code · 6 blank · 0 comment · 0 complexity · f88061e69b9d60b9f8ac3f3c8054fa5c 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 [ rgTDTtest1.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 rgTDTtest1
    18. 

  18. 	--mind 0.5
    19. 

  19. 	--tdt
    20. 

  20. 

  21. Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
    22. 

  22. 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
    23. 

  23. Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    24. 

  24. 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    25. 

  25. 40 individuals with nonmissing phenotypes
    26. 

  26. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    27. 

  27. Missing phenotype value is also -9
    28. 

  28. 10 cases, 30 controls and 0 missing
    29. 

  29. 21 males, 19 females, and 0 of unspecified sex
    30. 

  30. Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
    31. 

  31. Detected that binary PED file is v1.00 SNP-major mode
    32. 

  32. Before frequency and genotyping pruning, there are 25 SNPs
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  33. 27 founders and 13 non-founders found
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  34. 0 of 40 individuals removed for low genotyping ( MIND > 0.5 )
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  35. Total genotyping rate in remaining individuals is 0.995
    36. 

  36. 0 SNPs failed missingness test ( GENO > 1 )
    37. 

  37. 0 SNPs failed frequency test ( MAF < 0 )
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  38. After frequency and genotyping pruning, there are 25 SNPs
    39. 

  39. After filtering, 10 cases, 30 controls and 0 missing
    40. 

  40. After filtering, 21 males, 19 females, and 0 of unspecified sex
    41. 

  41. 14 nuclear families, 1 founder singletons found
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  42. 13 non-founders with 2 parents in 13 nuclear families
    43. 

  43. 0 non-founders without 2 parents in 0 nuclear families
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  44. 10 affected offspring trios
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  45. 0 phenotypically discordant parent pairs found
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  46. Converting data to Individual-major format
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  47. 0 Mendel errors detected in total
    48. 

  48. Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] 
    49. 

  49. 

  50. Analysis finished: Sun May  9 21:23:49 2010
    51. 

  51. 

  52. ###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439
    53.