This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CACTCT -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 97.98 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 3,193,041 Reads with adapters: 385,025 (12.1%) Reads that were too short: 21,275 (0.7%) Reads written (passing filters): 363,750 (11.4%) Total basepairs processed: 961,105,341 bp Total written (filtered): 54,924,000 bp (5.7%) === Adapter 1 === Sequence: CACTCT; Type: regular 5'; Length: 6; Trimmed: 385025 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 327 779.6 0 327 7 3869 779.6 0 3869 8 208 779.6 0 208 9 13363 779.6 0 13363 10 35 779.6 0 35 11 14 779.6 0 14 12 17 779.6 0 17 13 12 779.6 0 12 14 10 779.6 0 10 15 14 779.6 0 14 16 10 779.6 0 10 17 21 779.6 0 21 18 32 779.6 0 32 19 11 779.6 0 11 20 6 779.6 0 6 21 7 779.6 0 7 22 9 779.6 0 9 23 18 779.6 0 18 24 6 779.6 0 6 25 7 779.6 0 7 26 11 779.6 0 11 27 6 779.6 0 6 28 15 779.6 0 15 29 6 779.6 0 6 30 10 779.6 0 10 31 26 779.6 0 26 32 38 779.6 0 38 33 20 779.6 0 20 34 34 779.6 0 34 35 330 779.6 0 330 36 12 779.6 0 12 37 27 779.6 0 27 38 9 779.6 0 9 39 13 779.6 0 13 40 13 779.6 0 13 41 10 779.6 0 10 42 116 779.6 0 116 43 13 779.6 0 13 44 17 779.6 0 17 45 29 779.6 0 29 46 136 779.6 0 136 47 247 779.6 0 247 48 165 779.6 0 165 49 42 779.6 0 42 50 135 779.6 0 135 51 17 779.6 0 17 52 17 779.6 0 17 53 16 779.6 0 16 54 114 779.6 0 114 55 36 779.6 0 36 56 44 779.6 0 44 57 14 779.6 0 14 58 15 779.6 0 15 59 23 779.6 0 23 60 12 779.6 0 12 61 15 779.6 0 15 62 33 779.6 0 33 63 15 779.6 0 15 64 9 779.6 0 9 65 11 779.6 0 11 66 12 779.6 0 12 67 25 779.6 0 25 68 7 779.6 0 7 69 14 779.6 0 14 70 27 779.6 0 27 71 19 779.6 0 19 72 3 779.6 0 3 73 8 779.6 0 8 74 12 779.6 0 12 75 3 779.6 0 3 76 7 779.6 0 7 77 13 779.6 0 13 78 14 779.6 0 14 79 22 779.6 0 22 80 22 779.6 0 22 81 16 779.6 0 16 82 38 779.6 0 38 83 39 779.6 0 39 84 31 779.6 0 31 85 11 779.6 0 11 86 10 779.6 0 10 87 18 779.6 0 18 88 18 779.6 0 18 89 33 779.6 0 33 90 62 779.6 0 62 91 9 779.6 0 9 92 143 779.6 0 143 93 59 779.6 0 59 94 165 779.6 0 165 95 58 779.6 0 58 96 45 779.6 0 45 97 43 779.6 0 43 98 41 779.6 0 41 99 34 779.6 0 34 100 48 779.6 0 48 101 21 779.6 0 21 102 67 779.6 0 67 103 52 779.6 0 52 104 176 779.6 0 176 105 528 779.6 0 528 106 655 779.6 0 655 107 42 779.6 0 42 108 99 779.6 0 99 109 93 779.6 0 93 110 139 779.6 0 139 111 55 779.6 0 55 112 204 779.6 0 204 113 99 779.6 0 99 114 114 779.6 0 114 115 32 779.6 0 32 116 37 779.6 0 37 117 40 779.6 0 40 118 56 779.6 0 56 119 138 779.6 0 138 120 41 779.6 0 41 121 46 779.6 0 46 122 59 779.6 0 59 123 31 779.6 0 31 124 122 779.6 0 122 125 127 779.6 0 127 126 89 779.6 0 89 127 235 779.6 0 235 128 258 779.6 0 258 129 419 779.6 0 419 130 136 779.6 0 136 131 247 779.6 0 247 132 78 779.6 0 78 133 157 779.6 0 157 134 878 779.6 0 878 135 219 779.6 0 219 136 217 779.6 0 217 137 92 779.6 0 92 138 104 779.6 0 104 139 184 779.6 0 184 140 247 779.6 0 247 141 296 779.6 0 296 142 354 779.6 0 354 143 643 779.6 0 643 144 1721 779.6 0 1721 145 1623 779.6 0 1623 146 22266 779.6 0 22266 147 10971 779.6 0 10971 148 26982 779.6 0 26982 149 514 779.6 0 514 150 291 779.6 0 291 151 912 779.6 0 912 152 1052 779.6 0 1052 153 2235 779.6 0 2235 154 430 779.6 0 430 155 499 779.6 0 499 156 826 779.6 0 826 157 1220 779.6 0 1220 158 1546 779.6 0 1546 159 3914 779.6 0 3914 160 6416 779.6 0 6416 161 104459 779.6 0 104459 162 62973 779.6 0 62973 163 79950 779.6 0 79950 164 552 779.6 0 552 165 230 779.6 0 230 166 156 779.6 0 156 167 145 779.6 0 145 168 57 779.6 0 57 169 40 779.6 0 40 170 33 779.6 0 33 171 46 779.6 0 46 172 68 779.6 0 68 173 107 779.6 0 107 174 79 779.6 0 79 175 46 779.6 0 46 176 54 779.6 0 54 177 45 779.6 0 45 178 38 779.6 0 38 179 92 779.6 0 92 180 82 779.6 0 82 181 145 779.6 0 145 182 299 779.6 0 299 183 369 779.6 0 369 184 169 779.6 0 169 185 72 779.6 0 72 186 50 779.6 0 50 187 170 779.6 0 170 188 40 779.6 0 40 189 78 779.6 0 78 190 85 779.6 0 85 191 85 779.6 0 85 192 127 779.6 0 127 193 62 779.6 0 62 194 55 779.6 0 55 195 31 779.6 0 31 196 62 779.6 0 62 197 58 779.6 0 58 198 67 779.6 0 67 199 50 779.6 0 50 200 28 779.6 0 28 201 56 779.6 0 56 202 132 779.6 0 132 203 107 779.6 0 107 204 111 779.6 0 111 205 58 779.6 0 58 206 79 779.6 0 79 207 49 779.6 0 49 208 50 779.6 0 50 209 82 779.6 0 82 210 52 779.6 0 52 211 62 779.6 0 62 212 58 779.6 0 58 213 100 779.6 0 100 214 136 779.6 0 136 215 173 779.6 0 173 216 167 779.6 0 167 217 160 779.6 0 160 218 244 779.6 0 244 219 163 779.6 0 163 220 90 779.6 0 90 221 70 779.6 0 70 222 120 779.6 0 120 223 182 779.6 0 182 224 69 779.6 0 69 225 114 779.6 0 114 226 170 779.6 0 170 227 106 779.6 0 106 228 153 779.6 0 153 229 90 779.6 0 90 230 68 779.6 0 68 231 56 779.6 0 56 232 63 779.6 0 63 233 91 779.6 0 91 234 106 779.6 0 106 235 75 779.6 0 75 236 76 779.6 0 76 237 94 779.6 0 94 238 293 779.6 0 293 239 262 779.6 0 262 240 1582 779.6 0 1582 241 1769 779.6 0 1769 242 3852 779.6 0 3852 243 346 779.6 0 346 244 278 779.6 0 278 245 149 779.6 0 149 246 100 779.6 0 100 247 35 779.6 0 35 248 35 779.6 0 35 249 55 779.6 0 55 250 120 779.6 0 120 251 164 779.6 0 164 252 212 779.6 0 212 253 153 779.6 0 153 254 255 779.6 0 255 255 169 779.6 0 169 256 152 779.6 0 152 257 91 779.6 0 91 258 53 779.6 0 53 259 37 779.6 0 37 260 51 779.6 0 51 261 103 779.6 0 103 262 148 779.6 0 148 263 133 779.6 0 133 264 122 779.6 0 122 265 160 779.6 0 160 266 202 779.6 0 202 267 415 779.6 0 415 268 315 779.6 0 315 269 336 779.6 0 336 270 338 779.6 0 338 271 241 779.6 0 241 272 220 779.6 0 220 273 119 779.6 0 119 274 99 779.6 0 99 275 184 779.6 0 184 276 191 779.6 0 191 277 745 779.6 0 745 278 905 779.6 0 905 279 477 779.6 0 477 280 231 779.6 0 231 281 133 779.6 0 133 282 123 779.6 0 123 283 243 779.6 0 243 284 90 779.6 0 90 285 116 779.6 0 116 286 80 779.6 0 80 287 61 779.6 0 61 288 76 779.6 0 76 289 44 779.6 0 44 290 97 779.6 0 97 291 103 779.6 0 103 292 78 779.6 0 78 293 46 779.6 0 46 294 33 779.6 0 33 295 14 779.6 0 14 296 19 779.6 0 19 297 32 779.6 0 32 298 29 779.6 0 29 299 63 779.6 0 63 300 67 779.6 0 67 301 55 779.6 0 55 Finished in 13.93 s (38 us/read; 1.57 M reads/minute). === Summary === Total reads processed: 363,750 Reads with adapters: 4,161 (1.1%) Reads that were too short: 7 (0.0%) Reads written (passing filters): 4,154 (1.1%) Total basepairs processed: 54,924,000 bp Total written (filtered): 1,120,785 bp (2.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 4161 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 17 15 0.0 3 0 0 0 1 14 18 2 0.0 3 0 0 1 1 19 41 0.0 3 0 39 1 0 1 20 3885 0.0 4 3840 44 1 21 17 0.0 4 0 17 22 1 0.0 4 0 0 1 23 29 0.0 4 27 0 0 2 24 3 0.0 4 0 0 0 0 3 28 2 0.0 4 1 0 0 0 1 34 1 0.0 4 0 0 0 0 1 51 1 0.0 4 0 0 0 0 1 56 1 0.0 4 0 0 0 1 60 1 0.0 4 0 0 0 0 1 84 1 0.0 4 0 0 0 0 1 112 1 0.0 4 0 0 0 0 1 126 2 0.0 4 0 0 0 0 2 127 154 0.0 4 0 0 0 0 154 136 1 0.0 4 0 0 0 0 1 153 1 0.0 4 0 0 0 0 1 191 1 0.0 4 0 0 0 0 1 228 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 0.16 s (39 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 4,154 Reads with adapters: 2,078 (50.0%) Reads written (passing filters): 4,154 (100.0%) Total basepairs processed: 1,120,785 bp Total written (filtered): 561,753 bp (50.1%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2078 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.5% G: 0.0% T: 99.2% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "T" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 3 1 64.9 0 1 12 1 0.0 1 0 1 249 1 0.0 1 1 262 1 0.0 1 1 267 7 0.0 1 7 268 17 0.0 1 16 1 269 1452 0.0 1 1334 118 270 566 0.0 1 535 31 271 31 0.0 1 29 2 272 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.