/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. ###### SICER v1.1 ######
  3. #############################################
  4. Input library directory:
  5. ChIP library:
  6. Output directory:
  7. Species: mm8
  8. Threshold for redundancy allowed for reads: 1
  9. Window size: 200 bps
  10. Fragment size: 150 bps. The shift for reads is half of 150
  11. Effective genome size as a fraction of the reference genome of mm8: 0.740000
  12. Gap size: 600 bps
  13. Evalue for identification of significant islands: 0.01
  14. Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
  15. chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
  16. chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  17. chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  18. chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  19. chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  20. chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  21. chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  22. chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  23. chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  24. chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  25. chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  26. chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  27. chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  28. chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  29. chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  30. chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  31. chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  32. chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  33. chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  34. chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  35. chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  36. chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
  37. Partion the genome in windows ...
  38. Generate summary files for input_bed_file...
  39. total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
  40. total tag count in chr2.bed is: 0.0 = 0.0+0.0
  41. total tag count in chr3.bed is: 0.0 = 0.0+0.0
  42. total tag count in chr4.bed is: 0.0 = 0.0+0.0
  43. total tag count in chr5.bed is: 0.0 = 0.0+0.0
  44. total tag count in chr6.bed is: 0.0 = 0.0+0.0
  45. total tag count in chr7.bed is: 0.0 = 0.0+0.0
  46. total tag count in chr8.bed is: 0.0 = 0.0+0.0
  47. total tag count in chr9.bed is: 0.0 = 0.0+0.0
  48. total tag count in chr10.bed is: 0.0 = 0.0+0.0
  49. total tag count in chr11.bed is: 0.0 = 0.0+0.0
  50. total tag count in chr12.bed is: 0.0 = 0.0+0.0
  51. total tag count in chr13.bed is: 0.0 = 0.0+0.0
  52. total tag count in chr14.bed is: 0.0 = 0.0+0.0
  53. total tag count in chr15.bed is: 0.0 = 0.0+0.0
  54. total tag count in chr16.bed is: 0.0 = 0.0+0.0
  55. total tag count in chr17.bed is: 0.0 = 0.0+0.0
  56. total tag count in chr18.bed is: 0.0 = 0.0+0.0
  57. total tag count in chr19.bed is: 0.0 = 0.0+0.0
  58. total tag count in chrX.bed is: 0.0 = 0.0+0.0
  59. total tag count in chrY.bed is: 0.0 = 0.0+0.0
  60. total tag count in chrM.bed is: 0.0 = 0.0+0.0
  61. Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
  62. Convert the normalized summary graph into wig vstep format...
  63. Find significant islands with E-value 0.01 for input_bed_file...
  64. Species: mm8
  65. Window_size: 200
  66. Gap size: 600
  67. E value is: 0.01
  68. Total read count: 9898.0
  69. Genome Length: 2644093988
  70. Effective genome Length: 1956629551
  71. Window average: 0.0010117398048
  72. Window pvalue: 0.2
  73. Minimum num of tags in a qualified window: 1
  74. Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
  75. Determine the score threshold from random background
  76. The score threshold is: 21.384
  77. Make and write islands
  78. Total number of islands: 352
  79. Filter reads with identified significant islands for input_bed_file...
  80. Make summary graph with filtered reads for input_bed_file...
  81. total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
  82. total tag count in chr2.bed is: 0.0 = 0.0+0.0
  83. total tag count in chr3.bed is: 0.0 = 0.0+0.0
  84. total tag count in chr4.bed is: 0.0 = 0.0+0.0
  85. total tag count in chr5.bed is: 0.0 = 0.0+0.0
  86. total tag count in chr6.bed is: 0.0 = 0.0+0.0
  87. total tag count in chr7.bed is: 0.0 = 0.0+0.0
  88. total tag count in chr8.bed is: 0.0 = 0.0+0.0
  89. total tag count in chr9.bed is: 0.0 = 0.0+0.0
  90. total tag count in chr10.bed is: 0.0 = 0.0+0.0
  91. total tag count in chr11.bed is: 0.0 = 0.0+0.0
  92. total tag count in chr12.bed is: 0.0 = 0.0+0.0
  93. total tag count in chr13.bed is: 0.0 = 0.0+0.0
  94. total tag count in chr14.bed is: 0.0 = 0.0+0.0
  95. total tag count in chr15.bed is: 0.0 = 0.0+0.0
  96. total tag count in chr16.bed is: 0.0 = 0.0+0.0
  97. total tag count in chr17.bed is: 0.0 = 0.0+0.0
  98. total tag count in chr18.bed is: 0.0 = 0.0+0.0
  99. total tag count in chr19.bed is: 0.0 = 0.0+0.0
  100. total tag count in chrX.bed is: 0.0 = 0.0+0.0
  101. total tag count in chrY.bed is: 0.0 = 0.0+0.0
  102. total tag count in chrM.bed is: 0.0 = 0.0+0.0
  103. Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
  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. Done!
  106. Additionally, these warnings were reported:
  107. Warning: chr2 reads do not exist in
  108. Warning: chr3 reads do not exist in
  109. Warning: chr4 reads do not exist in
  110. Warning: chr5 reads do not exist in
  111. Warning: chr6 reads do not exist in
  112. Warning: chr7 reads do not exist in
  113. Warning: chr8 reads do not exist in
  114. Warning: chr9 reads do not exist in
  115. Warning: chr10 reads do not exist in
  116. Warning: chr11 reads do not exist in
  117. Warning: chr12 reads do not exist in
  118. Warning: chr13 reads do not exist in
  119. Warning: chr14 reads do not exist in
  120. Warning: chr15 reads do not exist in
  121. Warning: chr16 reads do not exist in
  122. Warning: chr17 reads do not exist in
  123. Warning: chr18 reads do not exist in
  124. Warning: chr19 reads do not exist in
  125. Warning: chrX reads do not exist in
  126. Warning: chrY reads do not exist in
  127. Warning: chrM reads do not exist in
  128. Warning: chr2 reads do not exist in
  129. Warning: chr3 reads do not exist in
  130. Warning: chr4 reads do not exist in
  131. Warning: chr5 reads do not exist in
  132. Warning: chr6 reads do not exist in
  133. Warning: chr7 reads do not exist in
  134. Warning: chr8 reads do not exist in
  135. Warning: chr9 reads do not exist in
  136. Warning: chr10 reads do not exist in
  137. Warning: chr11 reads do not exist in
  138. Warning: chr12 reads do not exist in
  139. Warning: chr13 reads do not exist in
  140. Warning: chr14 reads do not exist in
  141. Warning: chr15 reads do not exist in
  142. Warning: chr16 reads do not exist in
  143. Warning: chr17 reads do not exist in
  144. Warning: chr18 reads do not exist in
  145. Warning: chr19 reads do not exist in
  146. Warning: chrX reads do not exist in
  147. Warning: chrY reads do not exist in
  148. Warning: chrM reads do not exist in
  149. Warning: chr2 reads do not exist in
  150. Warning: chr3 reads do not exist in
  151. Warning: chr4 reads do not exist in
  152. Warning: chr5 reads do not exist in
  153. Warning: chr6 reads do not exist in
  154. Warning: chr7 reads do not exist in
  155. Warning: chr8 reads do not exist in
  156. Warning: chr9 reads do not exist in
  157. Warning: chr10 reads do not exist in
  158. Warning: chr11 reads do not exist in
  159. Warning: chr12 reads do not exist in
  160. Warning: chr13 reads do not exist in
  161. Warning: chr14 reads do not exist in
  162. Warning: chr15 reads do not exist in
  163. Warning: chr16 reads do not exist in
  164. Warning: chr17 reads do not exist in
  165. Warning: chr18 reads do not exist in
  166. Warning: chr19 reads do not exist in
  167. Warning: chrX reads do not exist in
  168. Warning: chrY reads do not exist in
  169. Warning: chrM reads do not exist in
  170. Warning: chr2 reads do not exist in
  171. Warning: chr3 reads do not exist in
  172. Warning: chr4 reads do not exist in
  173. Warning: chr5 reads do not exist in
  174. Warning: chr6 reads do not exist in
  175. Warning: chr7 reads do not exist in
  176. Warning: chr8 reads do not exist in
  177. Warning: chr9 reads do not exist in
  178. Warning: chr10 reads do not exist in
  179. Warning: chr11 reads do not exist in
  180. Warning: chr12 reads do not exist in
  181. Warning: chr13 reads do not exist in
  182. Warning: chr14 reads do not exist in
  183. Warning: chr15 reads do not exist in
  184. Warning: chr16 reads do not exist in
  185. Warning: chr17 reads do not exist in
  186. Warning: chr18 reads do not exist in
  187. Warning: chr19 reads do not exist in
  188. Warning: chrX reads do not exist in
  189. Warning: chrY reads do not exist in
  190. Warning: chrM reads do not exist in