/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log

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  1. ## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42
    2. 

  2. ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner
    3. 

  3. ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1
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  4. 

  5. @----------------------------------------------------------@
    6. 

  6. |        PLINK!       |     v1.07      |   10/Aug/2009     |
    7. 

  7. |----------------------------------------------------------|
    8. 

  8. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    9. 

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

  10. |  For documentation, citation & bug-report instructions:  |
    11. 

  11. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    12. 

  12. @----------------------------------------------------------@
    13. 

  13. 

  14. Skipping web check... [ --noweb ] 
    15. 

  15. Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
    16. 

  16. Analysis started: Sun May  9 21:23:42 2010
    17. 

  17. 

  18. Options in effect:
    19. 

  19. 	--noweb
    20. 

  20. 	--bfile /share/shared/galaxy/test-data/tinywga
    21. 

  21. 	--indep-pairwise 10000 5000 0.1
    22. 

  22. 	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    23. 

  23. 	--mind 1
    24. 

  24. 	--geno 1
    25. 

  25. 	--maf 0
    26. 

  26. 	--hwe 0
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  27. 	--me 1 1
    28. 

  28. 

  29. Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
    30. 

  30. 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
    31. 

  31. Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    32. 

  32. 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
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  33. 40 individuals with nonmissing phenotypes
    34. 

  34. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
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  35. Missing phenotype value is also -9
    36. 

  36. 10 cases, 30 controls and 0 missing
    37. 

  37. 21 males, 19 females, and 0 of unspecified sex
    38. 

  38. Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
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  39. Detected that binary PED file is v1.00 SNP-major mode
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  40. Before frequency and genotyping pruning, there are 25 SNPs
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  41. 27 founders and 13 non-founders found
    42. 

  42. 0 markers to be excluded based on HWE test ( p <= 0 )
    43. 

  43. 	0 markers failed HWE test in cases
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  44. 	0 markers failed HWE test in controls
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  45. Total genotyping rate in remaining individuals is 0.995
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  46. 0 SNPs failed missingness test ( GENO > 1 )
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  47. 0 SNPs failed frequency test ( MAF < 0 )
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  48. After frequency and genotyping pruning, there are 25 SNPs
    49. 

  49. After filtering, 10 cases, 30 controls and 0 missing
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  50. After filtering, 21 males, 19 females, and 0 of unspecified sex
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  51. 14 nuclear families, 1 founder singletons found
    52. 

  52. 13 non-founders with 2 parents in 13 nuclear families
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  53. 0 non-founders without 2 parents in 0 nuclear families
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  54. 10 affected offspring trios
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  55. 0 phenotypically discordant parent pairs found
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  56. Converting data to Individual-major format
    57. 

  57. Filtering SNPs/families for Mendel Error rates above 1, 1
    58. 

  58. 0 Mendel errors detected in total
    59. 

  59. 0 families ( 0 individuals ) removed due to Mendel errors
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  60. 0 markers removed due to Mendel errors, 25 remaining
    61. 

  61. Converting data to SNP-major format
    62. 

  62. Performing LD-based pruning...
    63. 

  63. Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ]
    64. 

  64. Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ]
    65. 

  65. Scanning from chromosome 22 to 22
    66. 

  66. 

  67. Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]
    68. 

  68. For chromosome 22, 22 SNPs pruned out, 3 remaining
    69. 

  69. 

  70. Analysis finished: Sun May  9 21:23:42 2010
    71. 

  71. 

  72. 

  73. ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    74. 

  74. 

  75. @----------------------------------------------------------@
    76. 

  76. |        PLINK!       |     v1.07      |   10/Aug/2009     |
    77. 

  77. |----------------------------------------------------------|
    78. 

  78. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    79. 

  79. |----------------------------------------------------------|
    80. 

  80. |  For documentation, citation & bug-report instructions:  |
    81. 

  81. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    82. 

  82. @----------------------------------------------------------@
    83. 

  83. 

  84. Skipping web check... [ --noweb ] 
    85. 

  85. Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
    86. 

  86. Analysis started: Sun May  9 21:23:42 2010
    87. 

  87. 

  88. Options in effect:
    89. 

  89. 	--noweb
    90. 

  90. 	--bfile /share/shared/galaxy/test-data/tinywga
    91. 

  91. 	--extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in
    92. 

  92. 	--make-bed
    93. 

  93. 	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    94. 

  94. 

  95. Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
    96. 

  96. 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
    97. 

  97. Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    98. 

  98. 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
    99. 

  99. 40 individuals with nonmissing phenotypes
    100. 

  100. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    101. 

  101. Missing phenotype value is also -9
    102. 

  102. 10 cases, 30 controls and 0 missing
    103. 

  103. 21 males, 19 females, and 0 of unspecified sex
    104. 

  104. Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
    105. 

  105. Detected that binary PED file is v1.00 SNP-major mode
    106. 

  106. Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read
    107. 

  107. Before frequency and genotyping pruning, there are 3 SNPs
    108. 

  108. 27 founders and 13 non-founders found
    109. 

  109. Total genotyping rate in remaining individuals is 1
    110. 

  110. 0 SNPs failed missingness test ( GENO > 1 )
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  111. 0 SNPs failed frequency test ( MAF < 0 )
    112. 

  112. After frequency and genotyping pruning, there are 3 SNPs
    113. 

  113. After filtering, 10 cases, 30 controls and 0 missing
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  114. After filtering, 21 males, 19 females, and 0 of unspecified sex
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  115. Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
    116. 

  116. Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
    117. 

  117. Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
    118. 

  118. Using (default) SNP-major mode
    119. 

  119. 

  120. Analysis finished: Sun May  9 21:23:42 2010
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  121. 

  122. 

  123. ## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    124. 

  124. 

  125. @----------------------------------------------------------@
    126. 

  126. |        PLINK!       |     v1.07      |   10/Aug/2009     |
    127. 

  127. |----------------------------------------------------------|
    128. 

  128. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    129. 

  129. |----------------------------------------------------------|
    130. 

  130. |  For documentation, citation & bug-report instructions:  |
    131. 

  131. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    132. 

  132. @----------------------------------------------------------@
    133. 

  133. 

  134. Skipping web check... [ --noweb ] 
    135. 

  135. Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
    136. 

  136. Analysis started: Sun May  9 21:23:42 2010
    137. 

  137. 

  138. Options in effect:
    139. 

  139. 	--noweb
    140. 

  140. 	--bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    141. 

  141. 	--recode
    142. 

  142. 	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    143. 

  143. 

  144. Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
    145. 

  145. 3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ]
    146. 

  146. Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
    147. 

  147. 40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
    148. 

  148. 40 individuals with nonmissing phenotypes
    149. 

  149. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    150. 

  150. Missing phenotype value is also -9
    151. 

  151. 10 cases, 30 controls and 0 missing
    152. 

  152. 21 males, 19 females, and 0 of unspecified sex
    153. 

  153. Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
    154. 

  154. Detected that binary PED file is v1.00 SNP-major mode
    155. 

  155. Before frequency and genotyping pruning, there are 3 SNPs
    156. 

  156. 27 founders and 13 non-founders found
    157. 

  157. Total genotyping rate in remaining individuals is 1
    158. 

  158. 0 SNPs failed missingness test ( GENO > 1 )
    159. 

  159. 0 SNPs failed frequency test ( MAF < 0 )
    160. 

  160. After frequency and genotyping pruning, there are 3 SNPs
    161. 

  161. After filtering, 10 cases, 30 controls and 0 missing
    162. 

  162. After filtering, 21 males, 19 females, and 0 of unspecified sex
    163. 

  163. Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] 
    164. 

  164. Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] 
    165. 

  165. 

  166. Analysis finished: Sun May  9 21:23:42 2010
    167.