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 139.39 s (47 us/read; 1.27 M reads/minute). === Summary === Total reads processed: 2,949,860 Reads with adapters: 125,649 (4.3%) Reads that were too short: 64,815 (2.2%) Reads written (passing filters): 60,834 (2.1%) Total basepairs processed: 887,907,860 bp Total written (filtered): 12,967,478 bp (1.5%) === Adapter 1 === Sequence: CGGCCA; Type: regular 5'; Length: 6; Trimmed: 125649 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 2803 720.2 0 2803 7 9274 720.2 0 9274 8 500 720.2 0 500 9 11838 720.2 0 11838 10 27 720.2 0 27 11 64 720.2 0 64 12 42 720.2 0 42 13 20 720.2 0 20 14 23 720.2 0 23 15 12 720.2 0 12 16 19 720.2 0 19 17 25 720.2 0 25 18 21 720.2 0 21 19 20 720.2 0 20 20 12 720.2 0 12 21 17 720.2 0 17 22 19 720.2 0 19 23 27 720.2 0 27 24 36 720.2 0 36 25 17 720.2 0 17 26 17 720.2 0 17 27 26 720.2 0 26 28 25 720.2 0 25 29 14 720.2 0 14 30 35 720.2 0 35 31 30 720.2 0 30 32 34 720.2 0 34 33 32 720.2 0 32 34 25 720.2 0 25 35 18 720.2 0 18 36 13 720.2 0 13 37 26 720.2 0 26 38 58 720.2 0 58 39 36 720.2 0 36 40 38 720.2 0 38 41 375 720.2 0 375 42 1127 720.2 0 1127 43 257 720.2 0 257 44 20 720.2 0 20 45 19 720.2 0 19 46 21 720.2 0 21 47 36 720.2 0 36 48 40 720.2 0 40 49 32 720.2 0 32 50 48 720.2 0 48 51 56 720.2 0 56 52 38 720.2 0 38 53 28 720.2 0 28 54 69 720.2 0 69 55 45 720.2 0 45 56 53 720.2 0 53 57 25 720.2 0 25 58 28 720.2 0 28 59 28 720.2 0 28 60 22 720.2 0 22 61 17 720.2 0 17 62 24 720.2 0 24 63 44 720.2 0 44 64 287 720.2 0 287 65 373 720.2 0 373 66 365 720.2 0 365 67 28 720.2 0 28 68 29 720.2 0 29 69 28 720.2 0 28 70 35 720.2 0 35 71 33 720.2 0 33 72 35 720.2 0 35 73 133 720.2 0 133 74 876 720.2 0 876 75 629 720.2 0 629 76 498 720.2 0 498 77 36 720.2 0 36 78 40 720.2 0 40 79 22 720.2 0 22 80 32 720.2 0 32 81 24 720.2 0 24 82 31 720.2 0 31 83 33 720.2 0 33 84 33 720.2 0 33 85 21 720.2 0 21 86 33 720.2 0 33 87 64 720.2 0 64 88 123 720.2 0 123 89 142 720.2 0 142 90 37 720.2 0 37 91 34 720.2 0 34 92 35 720.2 0 35 93 39 720.2 0 39 94 24 720.2 0 24 95 38 720.2 0 38 96 26 720.2 0 26 97 20 720.2 0 20 98 30 720.2 0 30 99 29 720.2 0 29 100 35 720.2 0 35 101 26 720.2 0 26 102 38 720.2 0 38 103 20 720.2 0 20 104 28 720.2 0 28 105 25 720.2 0 25 106 23 720.2 0 23 107 27 720.2 0 27 108 32 720.2 0 32 109 37 720.2 0 37 110 21 720.2 0 21 111 33 720.2 0 33 112 51 720.2 0 51 113 45 720.2 0 45 114 48 720.2 0 48 115 33 720.2 0 33 116 33 720.2 0 33 117 35 720.2 0 35 118 38 720.2 0 38 119 16 720.2 0 16 120 21 720.2 0 21 121 27 720.2 0 27 122 16 720.2 0 16 123 42 720.2 0 42 124 33 720.2 0 33 125 58 720.2 0 58 126 47 720.2 0 47 127 34 720.2 0 34 128 35 720.2 0 35 129 28 720.2 0 28 130 61 720.2 0 61 131 32 720.2 0 32 132 59 720.2 0 59 133 67 720.2 0 67 134 38 720.2 0 38 135 38 720.2 0 38 136 36 720.2 0 36 137 54 720.2 0 54 138 92 720.2 0 92 139 102 720.2 0 102 140 35 720.2 0 35 141 47 720.2 0 47 142 68 720.2 0 68 143 125 720.2 0 125 144 82 720.2 0 82 145 67 720.2 0 67 146 82 720.2 0 82 147 65 720.2 0 65 148 109 720.2 0 109 149 97 720.2 0 97 150 139 720.2 0 139 151 925 720.2 0 925 152 1956 720.2 0 1956 153 1311 720.2 0 1311 154 532 720.2 0 532 155 294 720.2 0 294 156 1138 720.2 0 1138 157 3686 720.2 0 3686 158 2863 720.2 0 2863 159 740 720.2 0 740 160 252 720.2 0 252 161 268 720.2 0 268 162 95 720.2 0 95 163 94 720.2 0 94 164 95 720.2 0 95 165 285 720.2 0 285 166 277 720.2 0 277 167 293 720.2 0 293 168 196 720.2 0 196 169 239 720.2 0 239 170 477 720.2 0 477 171 1072 720.2 0 1072 172 898 720.2 0 898 173 299 720.2 0 299 174 99 720.2 0 99 175 158 720.2 0 158 176 980 720.2 0 980 177 1915 720.2 0 1915 178 1738 720.2 0 1738 179 823 720.2 0 823 180 93 720.2 0 93 181 146 720.2 0 146 182 143 720.2 0 143 183 186 720.2 0 186 184 124 720.2 0 124 185 118 720.2 0 118 186 64 720.2 0 64 187 55 720.2 0 55 188 154 720.2 0 154 189 86 720.2 0 86 190 89 720.2 0 89 191 52 720.2 0 52 192 44 720.2 0 44 193 37 720.2 0 37 194 49 720.2 0 49 195 84 720.2 0 84 196 76 720.2 0 76 197 66 720.2 0 66 198 38 720.2 0 38 199 49 720.2 0 49 200 182 720.2 0 182 201 431 720.2 0 431 202 283 720.2 0 283 203 85 720.2 0 85 204 43 720.2 0 43 205 69 720.2 0 69 206 66 720.2 0 66 207 46 720.2 0 46 208 43 720.2 0 43 209 39 720.2 0 39 210 41 720.2 0 41 211 35 720.2 0 35 212 38 720.2 0 38 213 40 720.2 0 40 214 97 720.2 0 97 215 151 720.2 0 151 216 120 720.2 0 120 217 65 720.2 0 65 218 52 720.2 0 52 219 64 720.2 0 64 220 72 720.2 0 72 221 54 720.2 0 54 222 57 720.2 0 57 223 72 720.2 0 72 224 88 720.2 0 88 225 72 720.2 0 72 226 120 720.2 0 120 227 75 720.2 0 75 228 271 720.2 0 271 229 155 720.2 0 155 230 332 720.2 0 332 231 126 720.2 0 126 232 97 720.2 0 97 233 209 720.2 0 209 234 391 720.2 0 391 235 427 720.2 0 427 236 239 720.2 0 239 237 156 720.2 0 156 238 359 720.2 0 359 239 144 720.2 0 144 240 178 720.2 0 178 241 98 720.2 0 98 242 67 720.2 0 67 243 72 720.2 0 72 244 82 720.2 0 82 245 84 720.2 0 84 246 102 720.2 0 102 247 88 720.2 0 88 248 177 720.2 0 177 249 421 720.2 0 421 250 496 720.2 0 496 251 589 720.2 0 589 252 555 720.2 0 555 253 1612 720.2 0 1612 254 767 720.2 0 767 255 876 720.2 0 876 256 116 720.2 0 116 257 261 720.2 0 261 258 628 720.2 0 628 259 989 720.2 0 989 260 1140 720.2 0 1140 261 4406 720.2 0 4406 262 5745 720.2 0 5745 263 11680 720.2 0 11680 264 8153 720.2 0 8153 265 4828 720.2 0 4828 266 88 720.2 0 88 267 47 720.2 0 47 268 66 720.2 0 66 269 77 720.2 0 77 270 50 720.2 0 50 271 59 720.2 0 59 272 72 720.2 0 72 273 91 720.2 0 91 274 95 720.2 0 95 275 146 720.2 0 146 276 213 720.2 0 213 277 359 720.2 0 359 278 410 720.2 0 410 279 223 720.2 0 223 280 98 720.2 0 98 281 140 720.2 0 140 282 180 720.2 0 180 283 180 720.2 0 180 284 128 720.2 0 128 285 126 720.2 0 126 286 131 720.2 0 131 287 907 720.2 0 907 288 1920 720.2 0 1920 289 1077 720.2 0 1077 290 199 720.2 0 199 291 232 720.2 0 232 292 569 720.2 0 569 293 534 720.2 0 534 294 572 720.2 0 572 295 263 720.2 0 263 296 351 720.2 0 351 297 455 720.2 0 455 298 1540 720.2 0 1540 299 1608 720.2 0 1608 300 2200 720.2 0 2200 301 306 720.2 0 306 Finished in 4.15 s (68 us/read; 0.88 M reads/minute). === Summary === Total reads processed: 60,834 Reads with adapters: 11,980 (19.7%) Reads that were too short: 37 (0.1%) Reads written (passing filters): 11,943 (19.6%) Total basepairs processed: 12,967,478 bp Total written (filtered): 3,247,316 bp (25.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 11980 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 18 1 0.0 3 0 0 1 19 53 0.0 3 0 40 9 2 2 20 9875 0.0 4 9369 417 71 15 3 21 14 0.0 4 1 11 1 0 1 22 30 0.0 4 2 21 1 4 2 23 1761 0.0 4 1673 63 12 11 2 24 4 0.0 4 3 1 25 1 0.0 4 0 0 1 26 1 0.0 4 0 0 0 1 37 1 0.0 4 0 0 0 0 1 43 1 0.0 4 1 47 2 0.0 4 0 0 0 0 2 56 3 0.0 4 0 0 0 0 3 61 1 0.0 4 0 0 1 64 4 0.0 4 0 0 0 0 4 65 3 0.0 4 0 0 0 0 3 66 1 0.0 4 0 0 0 0 1 69 2 0.0 4 0 0 0 0 2 70 49 0.0 4 0 0 0 0 49 85 1 0.0 4 0 0 0 0 1 89 2 0.0 4 0 0 0 0 2 94 4 0.0 4 0 0 0 0 4 99 1 0.0 4 0 0 0 0 1 104 1 0.0 4 0 0 0 0 1 105 2 0.0 4 0 0 0 0 2 113 2 0.0 4 0 0 0 0 2 115 2 0.0 4 0 0 0 0 2 124 3 0.0 4 0 0 0 0 3 126 2 0.0 4 0 0 0 0 2 127 133 0.0 4 0 0 0 0 133 128 2 0.0 4 0 0 0 0 2 136 1 0.0 4 0 0 0 0 1 144 1 0.0 4 0 0 0 0 1 148 1 0.0 4 0 0 0 0 1 149 2 0.0 4 0 0 0 0 2 150 1 0.0 4 0 0 0 0 1 153 1 0.0 4 0 0 0 0 1 169 1 0.0 4 0 0 0 0 1 171 1 0.0 4 0 0 0 0 1 188 1 0.0 4 0 0 0 0 1 189 1 0.0 4 0 0 0 0 1 195 1 0.0 4 0 0 0 0 1 227 1 0.0 4 0 0 0 0 1 228 2 0.0 4 0 0 0 0 2 230 1 0.0 4 0 0 0 0 1 231 1 0.0 4 0 0 0 0 1 254 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 0.69 s (58 us/read; 1.04 M reads/minute). === Summary === Total reads processed: 11,943 Reads with adapters: 1,076 (9.0%) Reads written (passing filters): 11,943 (100.0%) Total basepairs processed: 3,247,316 bp Total written (filtered): 3,235,844 bp (99.6%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 1076 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 3.1% C: 7.8% G: 87.1% T: 2.0% none/other: 0.0% WARNING: The adapter is preceded by "G" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "G" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 3 36 186.6 0 36 4 6 46.7 0 6 5 2 11.7 0 2 9 132 0.0 0 3 129 10 246 0.0 1 16 230 11 535 0.0 1 14 521 12 114 0.0 1 0 114 13 1 0.0 1 0 1 15 1 0.0 1 0 1 20 1 0.0 1 1 171 1 0.0 1 1 210 1 0.0 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.