This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CGGCCA -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g ggactacnngggtatctaat -e 0.2 -O 20 - Trimming 1 adapter with at most 20.0% errors in single-end mode ... Finished in 58.17 s (26 us/read; 2.31 M reads/minute). === Summary === Total reads processed: 2,238,925 Reads with adapters: 55,977 (2.5%) Reads that were too short: 28,352 (1.3%) Reads written (passing filters): 27,625 (1.2%) Total basepairs processed: 673,916,425 bp Total written (filtered): 5,315,015 bp (0.8%) === Adapter 1 === Sequence: CGGCCA; Type: regular 5'; Length: 6; Trimmed: 55977 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 231 546.6 0 231 7 3239 546.6 0 3239 8 95 546.6 0 95 9 2643 546.6 0 2643 10 19 546.6 0 19 11 145 546.6 0 145 12 97 546.6 0 97 13 22 546.6 0 22 14 19 546.6 0 19 15 18 546.6 0 18 16 18 546.6 0 18 17 18 546.6 0 18 18 15 546.6 0 15 19 20 546.6 0 20 20 20 546.6 0 20 21 26 546.6 0 26 22 23 546.6 0 23 23 21 546.6 0 21 24 24 546.6 0 24 25 23 546.6 0 23 26 24 546.6 0 24 27 18 546.6 0 18 28 28 546.6 0 28 29 30 546.6 0 30 30 38 546.6 0 38 31 49 546.6 0 49 32 25 546.6 0 25 33 23 546.6 0 23 34 34 546.6 0 34 35 34 546.6 0 34 36 19 546.6 0 19 37 22 546.6 0 22 38 41 546.6 0 41 39 36 546.6 0 36 40 29 546.6 0 29 41 75 546.6 0 75 42 197 546.6 0 197 43 120 546.6 0 120 44 28 546.6 0 28 45 18 546.6 0 18 46 43 546.6 0 43 47 25 546.6 0 25 48 27 546.6 0 27 49 34 546.6 0 34 50 27 546.6 0 27 51 22 546.6 0 22 52 27 546.6 0 27 53 27 546.6 0 27 54 38 546.6 0 38 55 38 546.6 0 38 56 35 546.6 0 35 57 27 546.6 0 27 58 25 546.6 0 25 59 27 546.6 0 27 60 27 546.6 0 27 61 21 546.6 0 21 62 21 546.6 0 21 63 17 546.6 0 17 64 74 546.6 0 74 65 150 546.6 0 150 66 145 546.6 0 145 67 27 546.6 0 27 68 15 546.6 0 15 69 14 546.6 0 14 70 23 546.6 0 23 71 35 546.6 0 35 72 34 546.6 0 34 73 274 546.6 0 274 74 397 546.6 0 397 75 231 546.6 0 231 76 168 546.6 0 168 77 39 546.6 0 39 78 25 546.6 0 25 79 27 546.6 0 27 80 29 546.6 0 29 81 34 546.6 0 34 82 22 546.6 0 22 83 38 546.6 0 38 84 26 546.6 0 26 85 30 546.6 0 30 86 39 546.6 0 39 87 46 546.6 0 46 88 60 546.6 0 60 89 121 546.6 0 121 90 18 546.6 0 18 91 32 546.6 0 32 92 46 546.6 0 46 93 30 546.6 0 30 94 26 546.6 0 26 95 28 546.6 0 28 96 30 546.6 0 30 97 32 546.6 0 32 98 40 546.6 0 40 99 40 546.6 0 40 100 34 546.6 0 34 101 33 546.6 0 33 102 21 546.6 0 21 103 30 546.6 0 30 104 37 546.6 0 37 105 32 546.6 0 32 106 32 546.6 0 32 107 28 546.6 0 28 108 33 546.6 0 33 109 37 546.6 0 37 110 30 546.6 0 30 111 27 546.6 0 27 112 25 546.6 0 25 113 33 546.6 0 33 114 61 546.6 0 61 115 36 546.6 0 36 116 22 546.6 0 22 117 26 546.6 0 26 118 31 546.6 0 31 119 33 546.6 0 33 120 28 546.6 0 28 121 23 546.6 0 23 122 34 546.6 0 34 123 21 546.6 0 21 124 35 546.6 0 35 125 24 546.6 0 24 126 27 546.6 0 27 127 42 546.6 0 42 128 36 546.6 0 36 129 53 546.6 0 53 130 49 546.6 0 49 131 33 546.6 0 33 132 44 546.6 0 44 133 35 546.6 0 35 134 38 546.6 0 38 135 28 546.6 0 28 136 36 546.6 0 36 137 56 546.6 0 56 138 45 546.6 0 45 139 37 546.6 0 37 140 35 546.6 0 35 141 34 546.6 0 34 142 46 546.6 0 46 143 66 546.6 0 66 144 65 546.6 0 65 145 58 546.6 0 58 146 49 546.6 0 49 147 52 546.6 0 52 148 51 546.6 0 51 149 72 546.6 0 72 150 82 546.6 0 82 151 374 546.6 0 374 152 1070 546.6 0 1070 153 814 546.6 0 814 154 181 546.6 0 181 155 236 546.6 0 236 156 1545 546.6 0 1545 157 2473 546.6 0 2473 158 3605 546.6 0 3605 159 306 546.6 0 306 160 103 546.6 0 103 161 105 546.6 0 105 162 44 546.6 0 44 163 67 546.6 0 67 164 51 546.6 0 51 165 128 546.6 0 128 166 192 546.6 0 192 167 192 546.6 0 192 168 167 546.6 0 167 169 127 546.6 0 127 170 288 546.6 0 288 171 256 546.6 0 256 172 273 546.6 0 273 173 67 546.6 0 67 174 46 546.6 0 46 175 46 546.6 0 46 176 236 546.6 0 236 177 419 546.6 0 419 178 594 546.6 0 594 179 255 546.6 0 255 180 31 546.6 0 31 181 40 546.6 0 40 182 38 546.6 0 38 183 33 546.6 0 33 184 43 546.6 0 43 185 37 546.6 0 37 186 43 546.6 0 43 187 27 546.6 0 27 188 52 546.6 0 52 189 41 546.6 0 41 190 52 546.6 0 52 191 32 546.6 0 32 192 17 546.6 0 17 193 23 546.6 0 23 194 20 546.6 0 20 195 26 546.6 0 26 196 43 546.6 0 43 197 27 546.6 0 27 198 30 546.6 0 30 199 39 546.6 0 39 200 68 546.6 0 68 201 51 546.6 0 51 202 61 546.6 0 61 203 38 546.6 0 38 204 14 546.6 0 14 205 22 546.6 0 22 206 26 546.6 0 26 207 21 546.6 0 21 208 20 546.6 0 20 209 23 546.6 0 23 210 35 546.6 0 35 211 29 546.6 0 29 212 25 546.6 0 25 213 27 546.6 0 27 214 44 546.6 0 44 215 47 546.6 0 47 216 56 546.6 0 56 217 35 546.6 0 35 218 31 546.6 0 31 219 30 546.6 0 30 220 37 546.6 0 37 221 21 546.6 0 21 222 18 546.6 0 18 223 46 546.6 0 46 224 122 546.6 0 122 225 54 546.6 0 54 226 42 546.6 0 42 227 28 546.6 0 28 228 98 546.6 0 98 229 49 546.6 0 49 230 138 546.6 0 138 231 57 546.6 0 57 232 48 546.6 0 48 233 100 546.6 0 100 234 263 546.6 0 263 235 374 546.6 0 374 236 125 546.6 0 125 237 131 546.6 0 131 238 94 546.6 0 94 239 51 546.6 0 51 240 69 546.6 0 69 241 40 546.6 0 40 242 27 546.6 0 27 243 34 546.6 0 34 244 40 546.6 0 40 245 45 546.6 0 45 246 40 546.6 0 40 247 40 546.6 0 40 248 97 546.6 0 97 249 208 546.6 0 208 250 140 546.6 0 140 251 148 546.6 0 148 252 77 546.6 0 77 253 1198 546.6 0 1198 254 475 546.6 0 475 255 671 546.6 0 671 256 74 546.6 0 74 257 135 546.6 0 135 258 323 546.6 0 323 259 478 546.6 0 478 260 742 546.6 0 742 261 2077 546.6 0 2077 262 2690 546.6 0 2690 263 5441 546.6 0 5441 264 2780 546.6 0 2780 265 1175 546.6 0 1175 266 47 546.6 0 47 267 40 546.6 0 40 268 32 546.6 0 32 269 27 546.6 0 27 270 28 546.6 0 28 271 21 546.6 0 21 272 45 546.6 0 45 273 29 546.6 0 29 274 40 546.6 0 40 275 37 546.6 0 37 276 48 546.6 0 48 277 95 546.6 0 95 278 159 546.6 0 159 279 130 546.6 0 130 280 36 546.6 0 36 281 41 546.6 0 41 282 69 546.6 0 69 283 77 546.6 0 77 284 51 546.6 0 51 285 49 546.6 0 49 286 44 546.6 0 44 287 373 546.6 0 373 288 241 546.6 0 241 289 448 546.6 0 448 290 104 546.6 0 104 291 74 546.6 0 74 292 212 546.6 0 212 293 158 546.6 0 158 294 92 546.6 0 92 295 82 546.6 0 82 296 97 546.6 0 97 297 160 546.6 0 160 298 1036 546.6 0 1036 299 1103 546.6 0 1103 300 1227 546.6 0 1227 301 56 546.6 0 56 Finished in 1.15 s (42 us/read; 1.44 M reads/minute). === Summary === Total reads processed: 27,625 Reads with adapters: 3,387 (12.3%) Reads that were too short: 10 (0.0%) Reads written (passing filters): 3,377 (12.2%) Total basepairs processed: 5,315,015 bp Total written (filtered): 922,725 bp (17.4%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 3387 times. No. of allowed errors: 0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20 bp: 4 Overview of removed sequences length count expect max.err error counts 19 18 0.0 3 0 17 1 20 3321 0.0 4 3270 51 21 6 0.0 4 3 3 23 7 0.0 4 0 0 0 7 36 1 0.0 4 0 0 0 0 1 64 2 0.0 4 0 0 0 0 2 65 2 0.0 4 0 0 0 0 2 66 1 0.0 4 0 0 0 0 1 70 7 0.0 4 0 0 0 0 7 75 1 0.0 4 0 0 0 0 1 77 1 0.0 4 0 0 0 0 1 100 1 0.0 4 0 0 0 0 1 114 1 0.0 4 0 0 0 0 1 127 16 0.0 4 0 0 0 0 16 144 1 0.0 4 0 0 0 0 1 206 1 0.0 4 0 0 0 0 1 This is cutadapt 1.11 with Python 2.7.12 Command line parameters: -a CTGSTGCVYCCCRTAGG - Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.11 s (33 us/read; 1.84 M reads/minute). === Summary === Total reads processed: 3,377 Reads with adapters: 73 (2.2%) Reads written (passing filters): 3,377 (100.0%) Total basepairs processed: 922,725 bp Total written (filtered): 920,863 bp (99.8%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 73 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 15.1% C: 5.5% G: 71.2% T: 8.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 12 52.8 0 12 4 1 13.2 0 1 10 3 0.0 1 0 3 11 45 0.0 1 0 45 12 5 0.0 1 0 5 13 1 0.0 1 0 1 121 1 0.0 1 1 191 1 0.0 1 0 1 225 2 0.0 1 2 231 2 0.0 1 2