/test-data/peakcalling_sicer/test_1/output_log_file.contains

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 190 lines · 190 code · 0 blank · 0 comment · 0 complexity · 6c634e618a1e1227946f68b58b81a15a MD5 · raw file 

    

  1. #############################################
    2. 

  2. ######           SICER v1.1            ######
    3. 

  3. #############################################
    4. 

  4. Input library directory:
    5. 

  5. ChIP library:
    6. 

  6. Output directory:
    7. 

  7. Species: mm8
    8. 

  8. Threshold for redundancy allowed for reads: 1
    9. 

  9. Window size: 200 bps
    10. 

  10. Fragment size: 150 bps. The shift for reads is half of 150
    11. 

  11. Effective genome size as a fraction of the reference genome of mm8: 0.740000
    12. 

  12. Gap size: 600 bps
    13. 

  13. Evalue for identification of significant islands: 0.01
    14. 

  14. Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
    15. 

  15. chr1 	Plus reads: 4989 	Retained plus reads: 4935 ;	Minus reads: 5011 	Retained minus reads: 4963
    16. 

  16. chr2 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    17. 

  17. chr3 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    18. 

  18. chr4 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    19. 

  19. chr5 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    20. 

  20. chr6 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    21. 

  21. chr7 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    22. 

  22. chr8 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    23. 

  23. chr9 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    24. 

  24. chr10 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    25. 

  25. chr11 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    26. 

  26. chr12 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    27. 

  27. chr13 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    28. 

  28. chr14 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    29. 

  29. chr15 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    30. 

  30. chr16 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    31. 

  31. chr17 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    32. 

  32. chr18 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    33. 

  33. chr19 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    34. 

  34. chrX 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    35. 

  35. chrY 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    36. 

  36. chrM 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
    37. 

  37. Partion the genome in windows ...
    38. 

  38. Generate summary files for input_bed_file...
    39. 

  39. total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
    40. 

  40. total tag count in chr2.bed is: 0.0 = 0.0+0.0
    41. 

  41. total tag count in chr3.bed is: 0.0 = 0.0+0.0
    42. 

  42. total tag count in chr4.bed is: 0.0 = 0.0+0.0
    43. 

  43. total tag count in chr5.bed is: 0.0 = 0.0+0.0
    44. 

  44. total tag count in chr6.bed is: 0.0 = 0.0+0.0
    45. 

  45. total tag count in chr7.bed is: 0.0 = 0.0+0.0
    46. 

  46. total tag count in chr8.bed is: 0.0 = 0.0+0.0
    47. 

  47. total tag count in chr9.bed is: 0.0 = 0.0+0.0
    48. 

  48. total tag count in chr10.bed is: 0.0 = 0.0+0.0
    49. 

  49. total tag count in chr11.bed is: 0.0 = 0.0+0.0
    50. 

  50. total tag count in chr12.bed is: 0.0 = 0.0+0.0
    51. 

  51. total tag count in chr13.bed is: 0.0 = 0.0+0.0
    52. 

  52. total tag count in chr14.bed is: 0.0 = 0.0+0.0
    53. 

  53. total tag count in chr15.bed is: 0.0 = 0.0+0.0
    54. 

  54. total tag count in chr16.bed is: 0.0 = 0.0+0.0
    55. 

  55. total tag count in chr17.bed is: 0.0 = 0.0+0.0
    56. 

  56. total tag count in chr18.bed is: 0.0 = 0.0+0.0
    57. 

  57. total tag count in chr19.bed is: 0.0 = 0.0+0.0
    58. 

  58. total tag count in chrX.bed is: 0.0 = 0.0+0.0
    59. 

  59. total tag count in chrY.bed is: 0.0 = 0.0+0.0
    60. 

  60. total tag count in chrM.bed is: 0.0 = 0.0+0.0
    61. 

  61. Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
    62. 

  62. Convert the normalized summary graph into wig vstep format...
    63. 

  63. Find significant islands with E-value 0.01 for input_bed_file...
    64. 

  64. Species:  mm8
    65. 

  65. Window_size:  200
    66. 

  66. Gap size:  600
    67. 

  67. E value is: 0.01
    68. 

  68. Total read count: 9898.0
    69. 

  69. Genome Length:  2644093988
    70. 

  70. Effective genome Length:  1956629551
    71. 

  71. Window average: 0.0010117398048
    72. 

  72. Window pvalue: 0.2
    73. 

  73. Minimum num of tags in a qualified window:  1
    74. 

  74. Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows 
    75. 

  75. Determine the score threshold from random background
    76. 

  76. The score threshold is:  21.384
    77. 

  77. Make and write islands
    78. 

  78. Total number of islands:  352
    79. 

  79. Filter reads with identified significant islands for input_bed_file...
    80. 

  80. Make summary graph with filtered reads for input_bed_file...
    81. 

  81. total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
    82. 

  82. total tag count in chr2.bed is: 0.0 = 0.0+0.0
    83. 

  83. total tag count in chr3.bed is: 0.0 = 0.0+0.0
    84. 

  84. total tag count in chr4.bed is: 0.0 = 0.0+0.0
    85. 

  85. total tag count in chr5.bed is: 0.0 = 0.0+0.0
    86. 

  86. total tag count in chr6.bed is: 0.0 = 0.0+0.0
    87. 

  87. total tag count in chr7.bed is: 0.0 = 0.0+0.0
    88. 

  88. total tag count in chr8.bed is: 0.0 = 0.0+0.0
    89. 

  89. total tag count in chr9.bed is: 0.0 = 0.0+0.0
    90. 

  90. total tag count in chr10.bed is: 0.0 = 0.0+0.0
    91. 

  91. total tag count in chr11.bed is: 0.0 = 0.0+0.0
    92. 

  92. total tag count in chr12.bed is: 0.0 = 0.0+0.0
    93. 

  93. total tag count in chr13.bed is: 0.0 = 0.0+0.0
    94. 

  94. total tag count in chr14.bed is: 0.0 = 0.0+0.0
    95. 

  95. total tag count in chr15.bed is: 0.0 = 0.0+0.0
    96. 

  96. total tag count in chr16.bed is: 0.0 = 0.0+0.0
    97. 

  97. total tag count in chr17.bed is: 0.0 = 0.0+0.0
    98. 

  98. total tag count in chr18.bed is: 0.0 = 0.0+0.0
    99. 

  99. total tag count in chr19.bed is: 0.0 = 0.0+0.0
    100. 

  100. total tag count in chrX.bed is: 0.0 = 0.0+0.0
    101. 

  101. total tag count in chrY.bed is: 0.0 = 0.0+0.0
    102. 

  102. total tag count in chrM.bed is: 0.0 = 0.0+0.0
    103. 

  103. Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
    104. 

  104. Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
    105. 

  105. Done!
    106. 

  106. Additionally, these warnings were reported:
    107. 

  107. Warning: chr2 reads do not exist in
    108. 

  108. Warning: chr3 reads do not exist in
    109. 

  109. Warning: chr4 reads do not exist in
    110. 

  110. Warning: chr5 reads do not exist in
    111. 

  111. Warning: chr6 reads do not exist in
    112. 

  112. Warning: chr7 reads do not exist in
    113. 

  113. Warning: chr8 reads do not exist in
    114. 

  114. Warning: chr9 reads do not exist in
    115. 

  115. Warning: chr10 reads do not exist in
    116. 

  116. Warning: chr11 reads do not exist in
    117. 

  117. Warning: chr12 reads do not exist in
    118. 

  118. Warning: chr13 reads do not exist in
    119. 

  119. Warning: chr14 reads do not exist in
    120. 

  120. Warning: chr15 reads do not exist in
    121. 

  121. Warning: chr16 reads do not exist in
    122. 

  122. Warning: chr17 reads do not exist in
    123. 

  123. Warning: chr18 reads do not exist in
    124. 

  124. Warning: chr19 reads do not exist in
    125. 

  125. Warning: chrX reads do not exist in
    126. 

  126. Warning: chrY reads do not exist in
    127. 

  127. Warning: chrM reads do not exist in
    128. 

  128. Warning: chr2 reads do not exist in
    129. 

  129. Warning: chr3 reads do not exist in
    130. 

  130. Warning: chr4 reads do not exist in
    131. 

  131. Warning: chr5 reads do not exist in
    132. 

  132. Warning: chr6 reads do not exist in
    133. 

  133. Warning: chr7 reads do not exist in
    134. 

  134. Warning: chr8 reads do not exist in
    135. 

  135. Warning: chr9 reads do not exist in
    136. 

  136. Warning: chr10 reads do not exist in
    137. 

  137. Warning: chr11 reads do not exist in
    138. 

  138. Warning: chr12 reads do not exist in
    139. 

  139. Warning: chr13 reads do not exist in
    140. 

  140. Warning: chr14 reads do not exist in
    141. 

  141. Warning: chr15 reads do not exist in
    142. 

  142. Warning: chr16 reads do not exist in
    143. 

  143. Warning: chr17 reads do not exist in
    144. 

  144. Warning: chr18 reads do not exist in
    145. 

  145. Warning: chr19 reads do not exist in
    146. 

  146. Warning: chrX reads do not exist in
    147. 

  147. Warning: chrY reads do not exist in
    148. 

  148. Warning: chrM reads do not exist in
    149. 

  149. Warning: chr2 reads do not exist in
    150. 

  150. Warning: chr3 reads do not exist in
    151. 

  151. Warning: chr4 reads do not exist in
    152. 

  152. Warning: chr5 reads do not exist in
    153. 

  153. Warning: chr6 reads do not exist in
    154. 

  154. Warning: chr7 reads do not exist in
    155. 

  155. Warning: chr8 reads do not exist in
    156. 

  156. Warning: chr9 reads do not exist in
    157. 

  157. Warning: chr10 reads do not exist in
    158. 

  158. Warning: chr11 reads do not exist in
    159. 

  159. Warning: chr12 reads do not exist in
    160. 

  160. Warning: chr13 reads do not exist in
    161. 

  161. Warning: chr14 reads do not exist in
    162. 

  162. Warning: chr15 reads do not exist in
    163. 

  163. Warning: chr16 reads do not exist in
    164. 

  164. Warning: chr17 reads do not exist in
    165. 

  165. Warning: chr18 reads do not exist in
    166. 

  166. Warning: chr19 reads do not exist in
    167. 

  167. Warning: chrX reads do not exist in
    168. 

  168. Warning: chrY reads do not exist in
    169. 

  169. Warning: chrM reads do not exist in
    170. 

  170. Warning: chr2 reads do not exist in
    171. 

  171. Warning: chr3 reads do not exist in
    172. 

  172. Warning: chr4 reads do not exist in
    173. 

  173. Warning: chr5 reads do not exist in
    174. 

  174. Warning: chr6 reads do not exist in
    175. 

  175. Warning: chr7 reads do not exist in
    176. 

  176. Warning: chr8 reads do not exist in
    177. 

  177. Warning: chr9 reads do not exist in
    178. 

  178. Warning: chr10 reads do not exist in
    179. 

  179. Warning: chr11 reads do not exist in
    180. 

  180. Warning: chr12 reads do not exist in
    181. 

  181. Warning: chr13 reads do not exist in
    182. 

  182. Warning: chr14 reads do not exist in
    183. 

  183. Warning: chr15 reads do not exist in
    184. 

  184. Warning: chr16 reads do not exist in
    185. 

  185. Warning: chr17 reads do not exist in
    186. 

  186. Warning: chr18 reads do not exist in
    187. 

  187. Warning: chr19 reads do not exist in
    188. 

  188. Warning: chrX reads do not exist in
    189. 

  189. Warning: chrY reads do not exist in
    190. 

  190. Warning: chrM reads do not exist in
    191.