Mercurial > repos > devteam > sicer
comparison test-data/test_2_output_log_file.contains @ 3:ddebd5f4338b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 4d5b98367b51a9e2f2711d1ccea9753a415d973a
| author | devteam |
|---|---|
| date | Wed, 24 Oct 2018 11:30:33 -0400 |
| parents | |
| children |
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| 2:937bb12c0f5c | 3:ddebd5f4338b |
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| 1 ############################################# | |
| 2 ###### SICER v1.1 ###### | |
| 3 ############################################# | |
| 4 Input library directory: | |
| 5 ChIP library: input_bed_file.bed | |
| 6 Control library: input_control_file.bed | |
| 7 Output directory: | |
| 8 Species: mm8 | |
| 9 Threshold for redundancy allowed for chip reads: 1 | |
| 10 Threshold for redundancy allowed for control reads: 1 | |
| 11 Window size: 200 bps | |
| 12 Fragment size: 150 bps. The shift for reads is half of 150 | |
| 13 Effective genome size as a fraction of the reference genome of mm8: 0.740000 | |
| 14 Gap size: 600 bps | |
| 15 Evalue for identification of candidate islands that exhibit clustering: 1000 | |
| 16 False discovery rate controlling significance: 0.01 | |
| 17 Preprocess the raw input_bed_file file to remove redundancy with threshold 1... | |
| 18 chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963 | |
| 19 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 20 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 21 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 22 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 23 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 24 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 25 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 26 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 27 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 28 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 29 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 30 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 31 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 32 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 33 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 34 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 35 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 36 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 37 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 38 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 39 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 40 Preprocess the raw input_control_file file to remove redundancy with threshold 1... | |
| 41 chr1 Plus reads: 4980 Retained plus reads: 4937 ; Minus reads: 5020 Retained minus reads: 4959 | |
| 42 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 43 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 44 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 45 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 46 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 47 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 48 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 49 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 50 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 51 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 52 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 53 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 54 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 55 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 56 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 57 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 58 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 59 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 60 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 61 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 62 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 | |
| 63 Partion the genome in windows ... | |
| 64 Generate summary files ... | |
| 65 total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0 | |
| 66 total tag count in chr2.bed is: 0.0 = 0.0+0.0 | |
| 67 total tag count in chr3.bed is: 0.0 = 0.0+0.0 | |
| 68 total tag count in chr4.bed is: 0.0 = 0.0+0.0 | |
| 69 total tag count in chr5.bed is: 0.0 = 0.0+0.0 | |
| 70 total tag count in chr6.bed is: 0.0 = 0.0+0.0 | |
| 71 total tag count in chr7.bed is: 0.0 = 0.0+0.0 | |
| 72 total tag count in chr8.bed is: 0.0 = 0.0+0.0 | |
| 73 total tag count in chr9.bed is: 0.0 = 0.0+0.0 | |
| 74 total tag count in chr10.bed is: 0.0 = 0.0+0.0 | |
| 75 total tag count in chr11.bed is: 0.0 = 0.0+0.0 | |
| 76 total tag count in chr12.bed is: 0.0 = 0.0+0.0 | |
| 77 total tag count in chr13.bed is: 0.0 = 0.0+0.0 | |
| 78 total tag count in chr14.bed is: 0.0 = 0.0+0.0 | |
| 79 total tag count in chr15.bed is: 0.0 = 0.0+0.0 | |
| 80 total tag count in chr16.bed is: 0.0 = 0.0+0.0 | |
| 81 total tag count in chr17.bed is: 0.0 = 0.0+0.0 | |
| 82 total tag count in chr18.bed is: 0.0 = 0.0+0.0 | |
| 83 total tag count in chr19.bed is: 0.0 = 0.0+0.0 | |
| 84 total tag count in chrX.bed is: 0.0 = 0.0+0.0 | |
| 85 total tag count in chrY.bed is: 0.0 = 0.0+0.0 | |
| 86 total tag count in chrM.bed is: 0.0 = 0.0+0.0 | |
| 87 Normalize summary graph by total island filtered reads per million for input_bed_file ... | |
| 88 Convert the normalized summary graph into wig vstep format... | |
| 89 Find candidate islands exhibiting clustering ... | |
| 90 Species: mm8 | |
| 91 Window_size: 200 | |
| 92 Gap size: 600 | |
| 93 E value is: 1000.0 | |
| 94 Total read count: 9898.0 | |
| 95 Genome Length: 2644093988 | |
| 96 Effective genome Length: 1956629551 | |
| 97 Window average: 0.0010117398048 | |
| 98 Window pvalue: 0.2 | |
| 99 Minimum num of tags in a qualified window: 1 | |
| 100 Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows | |
| 101 Determine the score threshold from random background | |
| 102 The score threshold is: 6.898 | |
| 103 Make and write islands | |
| 104 Total number of islands: 417 | |
| 105 Calculate significance of candidate islands using the control library ... | |
| 106 chip library size 9898.0 | |
| 107 control library size 9896.0 | |
| 108 Total number of chip reads on islands is: 9811 | |
| 109 Total number of control reads on islands is: 8514 | |
| 110 Identify significant islands using FDR criterion ... | |
| 111 Given significance 0.01 , there are 184 significant islands | |
| 112 Convert island summary to island bed file of format chr start end ChIP-read-count | |
| 113 Filter reads with identified significant islands... | |
| 114 Make summary graph with filtered reads... | |
| 115 total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0 | |
| 116 total tag count in chr2.bed is: 0.0 = 0.0+0.0 | |
| 117 total tag count in chr3.bed is: 0.0 = 0.0+0.0 | |
| 118 total tag count in chr4.bed is: 0.0 = 0.0+0.0 | |
| 119 total tag count in chr5.bed is: 0.0 = 0.0+0.0 | |
| 120 total tag count in chr6.bed is: 0.0 = 0.0+0.0 | |
| 121 total tag count in chr7.bed is: 0.0 = 0.0+0.0 | |
| 122 total tag count in chr8.bed is: 0.0 = 0.0+0.0 | |
| 123 total tag count in chr9.bed is: 0.0 = 0.0+0.0 | |
| 124 total tag count in chr10.bed is: 0.0 = 0.0+0.0 | |
| 125 total tag count in chr11.bed is: 0.0 = 0.0+0.0 | |
| 126 total tag count in chr12.bed is: 0.0 = 0.0+0.0 | |
| 127 total tag count in chr13.bed is: 0.0 = 0.0+0.0 | |
| 128 total tag count in chr14.bed is: 0.0 = 0.0+0.0 | |
| 129 total tag count in chr15.bed is: 0.0 = 0.0+0.0 | |
| 130 total tag count in chr16.bed is: 0.0 = 0.0+0.0 | |
| 131 total tag count in chr17.bed is: 0.0 = 0.0+0.0 | |
| 132 total tag count in chr18.bed is: 0.0 = 0.0+0.0 | |
| 133 total tag count in chr19.bed is: 0.0 = 0.0+0.0 | |
| 134 total tag count in chrX.bed is: 0.0 = 0.0+0.0 | |
| 135 total tag count in chrY.bed is: 0.0 = 0.0+0.0 | |
| 136 total tag count in chrM.bed is: 0.0 = 0.0+0.0 | |
| 137 Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million... | |
| 138 Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million... | |
| 139 Done! | |
| 140 Additionally, these warnings were reported: | |
| 141 Warning: chr2 reads do not exist in | |
| 142 Warning: chr3 reads do not exist in | |
| 143 Warning: chr4 reads do not exist in | |
| 144 Warning: chr5 reads do not exist in | |
| 145 Warning: chr6 reads do not exist in | |
| 146 Warning: chr7 reads do not exist in | |
| 147 Warning: chr8 reads do not exist in | |
| 148 Warning: chr9 reads do not exist in | |
| 149 Warning: chr10 reads do not exist in | |
| 150 Warning: chr11 reads do not exist in | |
| 151 Warning: chr12 reads do not exist in | |
| 152 Warning: chr13 reads do not exist in | |
| 153 Warning: chr14 reads do not exist in | |
| 154 Warning: chr15 reads do not exist in | |
| 155 Warning: chr16 reads do not exist in | |
| 156 Warning: chr17 reads do not exist in | |
| 157 Warning: chr18 reads do not exist in | |
| 158 Warning: chr19 reads do not exist in | |
| 159 Warning: chrX reads do not exist in | |
| 160 Warning: chrY reads do not exist in | |
| 161 Warning: chrM reads do not exist in | |
| 162 Warning: chr2 reads do not exist in | |
| 163 Warning: chr3 reads do not exist in | |
| 164 Warning: chr4 reads do not exist in | |
| 165 Warning: chr5 reads do not exist in | |
| 166 Warning: chr6 reads do not exist in | |
| 167 Warning: chr7 reads do not exist in | |
| 168 Warning: chr8 reads do not exist in | |
| 169 Warning: chr9 reads do not exist in | |
| 170 Warning: chr10 reads do not exist in | |
| 171 Warning: chr11 reads do not exist in | |
| 172 Warning: chr12 reads do not exist in | |
| 173 Warning: chr13 reads do not exist in | |
| 174 Warning: chr14 reads do not exist in | |
| 175 Warning: chr15 reads do not exist in | |
| 176 Warning: chr16 reads do not exist in | |
| 177 Warning: chr17 reads do not exist in | |
| 178 Warning: chr18 reads do not exist in | |
| 179 Warning: chr19 reads do not exist in | |
| 180 Warning: chrX reads do not exist in | |
| 181 Warning: chrY reads do not exist in | |
| 182 Warning: chrM reads do not exist in | |
| 183 Warning: chr2 reads do not exist in | |
| 184 Warning: chr3 reads do not exist in | |
| 185 Warning: chr4 reads do not exist in | |
| 186 Warning: chr5 reads do not exist in | |
| 187 Warning: chr6 reads do not exist in | |
| 188 Warning: chr7 reads do not exist in | |
| 189 Warning: chr8 reads do not exist in | |
| 190 Warning: chr9 reads do not exist in | |
| 191 Warning: chr10 reads do not exist in | |
| 192 Warning: chr11 reads do not exist in | |
| 193 Warning: chr12 reads do not exist in | |
| 194 Warning: chr13 reads do not exist in | |
| 195 Warning: chr14 reads do not exist in | |
| 196 Warning: chr15 reads do not exist in | |
| 197 Warning: chr16 reads do not exist in | |
| 198 Warning: chr17 reads do not exist in | |
| 199 Warning: chr18 reads do not exist in | |
| 200 Warning: chr19 reads do not exist in | |
| 201 Warning: chrX reads do not exist in | |
| 202 Warning: chrY reads do not exist in | |
| 203 Warning: chrM reads do not exist in | |
| 204 Warning: chr2 reads do not exist in | |
| 205 Warning: chr3 reads do not exist in | |
| 206 Warning: chr4 reads do not exist in | |
| 207 Warning: chr5 reads do not exist in | |
| 208 Warning: chr6 reads do not exist in | |
| 209 Warning: chr7 reads do not exist in | |
| 210 Warning: chr8 reads do not exist in | |
| 211 Warning: chr9 reads do not exist in | |
| 212 Warning: chr10 reads do not exist in | |
| 213 Warning: chr11 reads do not exist in | |
| 214 Warning: chr12 reads do not exist in | |
| 215 Warning: chr13 reads do not exist in | |
| 216 Warning: chr14 reads do not exist in | |
| 217 Warning: chr15 reads do not exist in | |
| 218 Warning: chr16 reads do not exist in | |
| 219 Warning: chr17 reads do not exist in | |
| 220 Warning: chr18 reads do not exist in | |
| 221 Warning: chr19 reads do not exist in | |
| 222 Warning: chrX reads do not exist in | |
| 223 Warning: chrY reads do not exist in | |
| 224 Warning: chrM reads do not exist in | |
| 225 Warning: chr2 reads do not exist in | |
| 226 Warning: chr3 reads do not exist in | |
| 227 Warning: chr4 reads do not exist in | |
| 228 Warning: chr5 reads do not exist in | |
| 229 Warning: chr6 reads do not exist in | |
| 230 Warning: chr7 reads do not exist in | |
| 231 Warning: chr8 reads do not exist in | |
| 232 Warning: chr9 reads do not exist in | |
| 233 Warning: chr10 reads do not exist in | |
| 234 Warning: chr11 reads do not exist in | |
| 235 Warning: chr12 reads do not exist in | |
| 236 Warning: chr13 reads do not exist in | |
| 237 Warning: chr14 reads do not exist in | |
| 238 Warning: chr15 reads do not exist in | |
| 239 Warning: chr16 reads do not exist in | |
| 240 Warning: chr17 reads do not exist in | |
| 241 Warning: chr18 reads do not exist in | |
| 242 Warning: chr19 reads do not exist in | |
| 243 Warning: chrX reads do not exist in | |
| 244 Warning: chrY reads do not exist in | |
| 245 Warning: chrM reads do not exist in | |
| 246 Warning: chr2 reads do not exist in | |
| 247 Warning: chr3 reads do not exist in | |
| 248 Warning: chr4 reads do not exist in | |
| 249 Warning: chr5 reads do not exist in | |
| 250 Warning: chr6 reads do not exist in | |
| 251 Warning: chr7 reads do not exist in | |
| 252 Warning: chr8 reads do not exist in | |
| 253 Warning: chr9 reads do not exist in | |
| 254 Warning: chr10 reads do not exist in | |
| 255 Warning: chr11 reads do not exist in | |
| 256 Warning: chr12 reads do not exist in | |
| 257 Warning: chr13 reads do not exist in | |
| 258 Warning: chr14 reads do not exist in | |
| 259 Warning: chr15 reads do not exist in | |
| 260 Warning: chr16 reads do not exist in | |
| 261 Warning: chr17 reads do not exist in | |
| 262 Warning: chr18 reads do not exist in | |
| 263 Warning: chr19 reads do not exist in | |
| 264 Warning: chrX reads do not exist in | |
| 265 Warning: chrY reads do not exist in | |
| 266 Warning: chrM reads do not exist in | |
| 267 Warning: chr2 reads do not exist in | |
| 268 Warning: chr3 reads do not exist in | |
| 269 Warning: chr4 reads do not exist in | |
| 270 Warning: chr5 reads do not exist in | |
| 271 Warning: chr6 reads do not exist in | |
| 272 Warning: chr7 reads do not exist in | |
| 273 Warning: chr8 reads do not exist in | |
| 274 Warning: chr9 reads do not exist in | |
| 275 Warning: chr10 reads do not exist in | |
| 276 Warning: chr11 reads do not exist in | |
| 277 Warning: chr12 reads do not exist in | |
| 278 Warning: chr13 reads do not exist in | |
| 279 Warning: chr14 reads do not exist in | |
| 280 Warning: chr15 reads do not exist in | |
| 281 Warning: chr16 reads do not exist in | |
| 282 Warning: chr17 reads do not exist in | |
| 283 Warning: chr18 reads do not exist in | |
| 284 Warning: chr19 reads do not exist in | |
| 285 Warning: chrX reads do not exist in | |
| 286 Warning: chrY reads do not exist in | |
| 287 Warning: chrM reads do not exist in |