This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TGATCC -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 110.15 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 3,184,960 Reads with adapters: 619,880 (19.5%) Reads that were too short: 3,614 (0.1%) Reads written (passing filters): 616,266 (19.3%) Total basepairs processed: 958,672,960 bp Total written (filtered): 153,627,441 bp (16.0%) === Adapter 1 === Sequence: TGATCC; Type: regular 5'; Length: 6; Trimmed: 619880 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 711 777.6 0 711 7 12934 777.6 0 12934 8 1997 777.6 0 1997 9 8737 777.6 0 8737 10 50 777.6 0 50 11 67 777.6 0 67 12 354 777.6 0 354 13 26 777.6 0 26 14 17 777.6 0 17 15 22 777.6 0 22 16 35 777.6 0 35 17 78 777.6 0 78 18 25 777.6 0 25 19 119 777.6 0 119 20 71 777.6 0 71 21 207 777.6 0 207 22 391 777.6 0 391 23 81 777.6 0 81 24 165 777.6 0 165 25 192 777.6 0 192 26 103 777.6 0 103 27 334 777.6 0 334 28 233 777.6 0 233 29 239 777.6 0 239 30 120 777.6 0 120 31 182 777.6 0 182 32 254 777.6 0 254 33 402 777.6 0 402 34 746 777.6 0 746 35 1285 777.6 0 1285 36 1560 777.6 0 1560 37 2139 777.6 0 2139 38 3518 777.6 0 3518 39 72366 777.6 0 72366 40 59293 777.6 0 59293 41 53605 777.6 0 53605 42 740 777.6 0 740 43 885 777.6 0 885 44 1042 777.6 0 1042 45 1922 777.6 0 1922 46 4231 777.6 0 4231 47 668 777.6 0 668 48 977 777.6 0 977 49 2693 777.6 0 2693 50 1591 777.6 0 1591 51 1096 777.6 0 1096 52 2386 777.6 0 2386 53 1737 777.6 0 1737 54 3090 777.6 0 3090 55 1715 777.6 0 1715 56 2754 777.6 0 2754 57 2616 777.6 0 2616 58 4725 777.6 0 4725 59 69284 777.6 0 69284 60 154247 777.6 0 154247 61 128491 777.6 0 128491 62 579 777.6 0 579 63 17 777.6 0 17 64 9 777.6 0 9 65 5 777.6 0 5 66 3 777.6 0 3 67 8 777.6 0 8 68 4 777.6 0 4 69 6 777.6 0 6 70 7 777.6 0 7 71 16 777.6 0 16 72 98 777.6 0 98 73 433 777.6 0 433 74 109 777.6 0 109 75 14 777.6 0 14 76 3 777.6 0 3 77 4 777.6 0 4 78 2 777.6 0 2 79 2 777.6 0 2 80 5 777.6 0 5 81 4 777.6 0 4 82 12 777.6 0 12 83 17 777.6 0 17 84 3 777.6 0 3 85 5 777.6 0 5 86 3 777.6 0 3 87 2 777.6 0 2 88 6 777.6 0 6 89 17 777.6 0 17 90 1 777.6 0 1 91 9 777.6 0 9 92 8 777.6 0 8 93 7 777.6 0 7 94 9 777.6 0 9 95 10 777.6 0 10 96 7 777.6 0 7 97 18 777.6 0 18 98 48 777.6 0 48 99 96 777.6 0 96 100 5 777.6 0 5 101 188 777.6 0 188 102 196 777.6 0 196 103 242 777.6 0 242 104 26 777.6 0 26 105 23 777.6 0 23 106 9 777.6 0 9 107 5 777.6 0 5 108 9 777.6 0 9 109 10 777.6 0 10 110 13 777.6 0 13 111 137 777.6 0 137 112 103 777.6 0 103 113 437 777.6 0 437 114 4 777.6 0 4 115 3 777.6 0 3 116 3 777.6 0 3 117 86 777.6 0 86 118 15 777.6 0 15 119 23 777.6 0 23 120 8 777.6 0 8 121 10 777.6 0 10 122 14 777.6 0 14 123 10 777.6 0 10 124 32 777.6 0 32 125 306 777.6 0 306 126 70 777.6 0 70 127 61 777.6 0 61 128 49 777.6 0 49 129 24 777.6 0 24 130 29 777.6 0 29 131 16 777.6 0 16 132 19 777.6 0 19 133 25 777.6 0 25 134 17 777.6 0 17 135 10 777.6 0 10 136 14 777.6 0 14 137 22 777.6 0 22 138 19 777.6 0 19 139 14 777.6 0 14 140 6 777.6 0 6 141 9 777.6 0 9 142 5 777.6 0 5 143 39 777.6 0 39 144 4 777.6 0 4 145 10 777.6 0 10 146 9 777.6 0 9 147 24 777.6 0 24 148 21 777.6 0 21 149 10 777.6 0 10 150 7 777.6 0 7 151 6 777.6 0 6 152 11 777.6 0 11 153 6 777.6 0 6 154 9 777.6 0 9 155 9 777.6 0 9 156 33 777.6 0 33 157 76 777.6 0 76 158 98 777.6 0 98 159 191 777.6 0 191 160 89 777.6 0 89 161 128 777.6 0 128 162 80 777.6 0 80 163 40 777.6 0 40 164 37 777.6 0 37 165 9 777.6 0 9 166 21 777.6 0 21 167 12 777.6 0 12 168 36 777.6 0 36 169 205 777.6 0 205 170 75 777.6 0 75 171 32 777.6 0 32 172 24 777.6 0 24 173 5 777.6 0 5 174 10 777.6 0 10 175 3 777.6 0 3 176 15 777.6 0 15 177 17 777.6 0 17 178 31 777.6 0 31 179 19 777.6 0 19 180 7 777.6 0 7 181 13 777.6 0 13 182 12 777.6 0 12 183 70 777.6 0 70 184 52 777.6 0 52 185 33 777.6 0 33 186 15 777.6 0 15 187 35 777.6 0 35 188 79 777.6 0 79 189 46 777.6 0 46 190 9 777.6 0 9 191 10 777.6 0 10 192 18 777.6 0 18 193 19 777.6 0 19 194 13 777.6 0 13 195 20 777.6 0 20 196 30 777.6 0 30 197 77 777.6 0 77 198 252 777.6 0 252 199 191 777.6 0 191 200 309 777.6 0 309 201 25 777.6 0 25 202 8 777.6 0 8 203 3 777.6 0 3 204 16 777.6 0 16 205 39 777.6 0 39 206 22 777.6 0 22 207 17 777.6 0 17 208 29 777.6 0 29 209 17 777.6 0 17 210 10 777.6 0 10 211 11 777.6 0 11 212 16 777.6 0 16 213 22 777.6 0 22 214 32 777.6 0 32 215 28 777.6 0 28 216 21 777.6 0 21 217 16 777.6 0 16 218 14 777.6 0 14 219 18 777.6 0 18 220 22 777.6 0 22 221 15 777.6 0 15 222 55 777.6 0 55 223 45 777.6 0 45 224 62 777.6 0 62 225 134 777.6 0 134 226 606 777.6 0 606 227 166 777.6 0 166 228 516 777.6 0 516 229 293 777.6 0 293 230 64 777.6 0 64 231 5 777.6 0 5 232 4 777.6 0 4 233 10 777.6 0 10 234 10 777.6 0 10 235 9 777.6 0 9 236 8 777.6 0 8 237 11 777.6 0 11 238 19 777.6 0 19 239 14 777.6 0 14 240 9 777.6 0 9 241 9 777.6 0 9 242 16 777.6 0 16 243 5 777.6 0 5 244 12 777.6 0 12 245 12 777.6 0 12 246 9 777.6 0 9 247 9 777.6 0 9 248 9 777.6 0 9 249 11 777.6 0 11 250 10 777.6 0 10 251 14 777.6 0 14 252 10 777.6 0 10 253 29 777.6 0 29 254 33 777.6 0 33 255 35 777.6 0 35 256 43 777.6 0 43 257 28 777.6 0 28 258 17 777.6 0 17 259 9 777.6 0 9 260 15 777.6 0 15 261 17 777.6 0 17 262 10 777.6 0 10 263 46 777.6 0 46 264 59 777.6 0 59 265 42 777.6 0 42 266 7 777.6 0 7 267 5 777.6 0 5 268 4 777.6 0 4 269 10 777.6 0 10 270 13 777.6 0 13 271 8 777.6 0 8 272 20 777.6 0 20 273 25 777.6 0 25 274 54 777.6 0 54 275 75 777.6 0 75 276 28 777.6 0 28 277 26 777.6 0 26 278 7 777.6 0 7 279 12 777.6 0 12 280 10 777.6 0 10 281 17 777.6 0 17 282 33 777.6 0 33 283 21 777.6 0 21 284 12 777.6 0 12 285 31 777.6 0 31 286 10 777.6 0 10 287 11 777.6 0 11 288 11 777.6 0 11 289 19 777.6 0 19 290 40 777.6 0 40 291 28 777.6 0 28 292 20 777.6 0 20 293 22 777.6 0 22 294 2 777.6 0 2 295 17 777.6 0 17 296 10 777.6 0 10 297 6 777.6 0 6 298 9 777.6 0 9 299 30 777.6 0 30 300 25 777.6 0 25 301 11 777.6 0 11 Finished in 29.94 s (49 us/read; 1.24 M reads/minute). === Summary === Total reads processed: 616,266 Reads with adapters: 13,870 (2.3%) Reads that were too short: 109 (0.0%) Reads written (passing filters): 13,761 (2.2%) Total basepairs processed: 153,627,441 bp Total written (filtered): 3,748,848 bp (2.4%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 13870 times. No. of allowed errors: 0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-17 bp: 3 Overview of removed sequences length count expect max.err error counts 16 87 0.0 3 0 87 17 13243 0.0 3 12998 241 4 18 30 0.0 3 4 26 19 7 0.0 3 1 0 5 1 20 4 0.0 3 0 0 0 4 22 1 0.0 3 1 24 1 0.0 3 0 0 0 1 28 1 0.0 3 1 41 26 0.0 3 0 0 0 26 42 1 0.0 3 0 0 0 1 48 10 0.0 3 8 2 59 1 0.0 3 0 0 0 1 63 1 0.0 3 0 0 0 1 67 1 0.0 3 0 0 0 1 78 1 0.0 3 0 0 0 1 81 1 0.0 3 0 0 0 1 84 1 0.0 3 0 0 0 1 91 1 0.0 3 0 0 0 1 92 1 0.0 3 0 0 0 1 93 2 0.0 3 0 0 0 2 97 1 0.0 3 0 0 0 1 98 1 0.0 3 0 0 0 1 108 1 0.0 3 0 0 0 1 110 1 0.0 3 0 0 0 1 111 1 0.0 3 0 0 0 1 112 1 0.0 3 0 0 0 1 115 2 0.0 3 0 0 0 2 126 2 0.0 3 0 0 0 2 129 1 0.0 3 0 0 0 1 130 1 0.0 3 0 0 0 1 131 2 0.0 3 0 0 0 2 132 39 0.0 3 0 0 0 39 133 8 0.0 3 0 0 1 7 134 2 0.0 3 0 0 0 2 135 67 0.0 3 0 0 0 67 136 4 0.0 3 0 0 0 4 137 1 0.0 3 0 0 0 1 159 1 0.0 3 0 0 0 1 160 199 0.0 3 0 0 0 199 163 1 0.0 3 0 0 0 1 166 1 0.0 3 0 0 0 1 183 2 0.0 3 0 0 0 2 185 1 0.0 3 0 0 0 1 186 6 0.0 3 0 0 0 6 189 1 0.0 3 0 0 0 1 192 3 0.0 3 0 0 0 3 199 1 0.0 3 0 0 0 1 226 1 0.0 3 0 0 0 1 233 2 0.0 3 0 0 0 2 234 77 0.0 3 0 0 1 76 235 3 0.0 3 0 0 0 3 244 1 0.0 3 0 0 0 1 248 1 0.0 3 0 0 0 1 249 2 0.0 3 0 0 0 2 250 3 0.0 3 0 0 0 3 256 2 0.0 3 0 0 0 2 275 2 0.0 3 0 0 0 2 277 1 0.0 3 0 0 0 1 278 1 0.0 3 0 0 0 1 283 1 0.0 3 0 0 0 1 285 1 0.0 3 0 0 0 1 This is cutadapt 1.11 with Python 2.7.12 Command line parameters: -a taatctatgggnncatcagg - Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.62 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 13,761 Reads with adapters: 847 (6.2%) Reads written (passing filters): 13,761 (100.0%) Total basepairs processed: 3,748,848 bp Total written (filtered): 3,746,306 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 847 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 10.2% C: 81.0% G: 7.7% T: 1.2% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "C" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 3 846 215.0 0 846 4 1 53.8 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.