/test-data/rgtestouts/rgQC/ldp_tinywga.log

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 48 lines · 42 code · 6 blank · 0 comment · 0 complexity · 72d486b579ef4126370c435ba1e8c4a8 MD5 · raw file 

    

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

  2. |        PLINK!       |     v1.06      |   24/Apr/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/        |
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  8. @----------------------------------------------------------@
    9. 

  9. 

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

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

  12. Analysis started: Wed May 19 15:15:38 2010
    13. 

  13. 

  14. Options in effect:
    15. 

  15. 	--noweb
    16. 

  16. 	--bfile /opt/galaxy/test-data/tinywga
    17. 

  17. 	--extract tinywga.prune.in
    18. 

  18. 	--make-bed
    19. 

  19. 	--out ldp_tinywga
    20. 

  20. 

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

  25. 40 individuals with nonmissing phenotypes
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  26. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
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  27. Missing phenotype value is also -9
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  28. 10 cases, 30 controls and 0 missing
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  29. 21 males, 19 females, and 0 of unspecified sex
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  30. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
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  31. Detected that binary PED file is v1.00 SNP-major mode
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  32. Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read
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  33. Before frequency and genotyping pruning, there are 14 SNPs
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  34. 27 founders and 13 non-founders found
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  35. Total genotyping rate in remaining individuals is 0.991071
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  36. 0 SNPs failed missingness test ( GENO > 1 )
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  37. 0 SNPs failed frequency test ( MAF < 0 )
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  38. After frequency and genotyping pruning, there are 14 SNPs
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  39. After filtering, 10 cases, 30 controls and 0 missing
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  40. After filtering, 21 males, 19 females, and 0 of unspecified sex
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  41. Writing pedigree information to [ ldp_tinywga.fam ] 
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  42. Writing map (extended format) information to [ ldp_tinywga.bim ] 
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  43. Writing genotype bitfile to [ ldp_tinywga.bed ] 
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  44. Using (default) SNP-major mode
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  45. 

  46. Analysis finished: Wed May 19 15:15:38 2010
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