This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGAAGA -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 103.39 s (32 us/read; 1.85 M reads/minute). === Summary === Total reads processed: 3,193,041 Reads with adapters: 462,119 (14.5%) Reads that were too short: 47,709 (1.5%) Reads written (passing filters): 414,410 (13.0%) Total basepairs processed: 961,105,341 bp Total written (filtered): 70,649,030 bp (7.4%) === Adapter 1 === Sequence: AGAAGA; Type: regular 5'; Length: 6; Trimmed: 462119 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 352 779.6 0 352 7 22582 779.6 0 22582 8 73 779.6 0 73 9 138 779.6 0 138 10 36 779.6 0 36 11 94 779.6 0 94 12 36 779.6 0 36 13 58 779.6 0 58 14 36 779.6 0 36 15 50 779.6 0 50 16 49 779.6 0 49 17 59 779.6 0 59 18 236 779.6 0 236 19 158 779.6 0 158 20 209 779.6 0 209 21 23 779.6 0 23 22 27 779.6 0 27 23 58 779.6 0 58 24 52 779.6 0 52 25 56 779.6 0 56 26 60 779.6 0 60 27 49 779.6 0 49 28 70 779.6 0 70 29 76 779.6 0 76 30 103 779.6 0 103 31 15 779.6 0 15 32 32 779.6 0 32 33 29 779.6 0 29 34 46 779.6 0 46 35 33 779.6 0 33 36 24 779.6 0 24 37 35 779.6 0 35 38 40 779.6 0 40 39 44 779.6 0 44 40 61 779.6 0 61 41 33 779.6 0 33 42 33 779.6 0 33 43 41 779.6 0 41 44 25 779.6 0 25 45 26 779.6 0 26 46 29 779.6 0 29 47 20 779.6 0 20 48 33 779.6 0 33 49 29 779.6 0 29 50 32 779.6 0 32 51 25 779.6 0 25 52 26 779.6 0 26 53 96 779.6 0 96 54 47 779.6 0 47 55 73 779.6 0 73 56 468 779.6 0 468 57 49 779.6 0 49 58 32 779.6 0 32 59 23 779.6 0 23 60 27 779.6 0 27 61 46 779.6 0 46 62 37 779.6 0 37 63 30 779.6 0 30 64 33 779.6 0 33 65 26 779.6 0 26 66 36 779.6 0 36 67 48 779.6 0 48 68 65 779.6 0 65 69 108 779.6 0 108 70 99 779.6 0 99 71 50 779.6 0 50 72 46 779.6 0 46 73 30 779.6 0 30 74 46 779.6 0 46 75 39 779.6 0 39 76 56 779.6 0 56 77 52 779.6 0 52 78 125 779.6 0 125 79 396 779.6 0 396 80 560 779.6 0 560 81 1019 779.6 0 1019 82 537 779.6 0 537 83 1095 779.6 0 1095 84 1529 779.6 0 1529 85 5996 779.6 0 5996 86 5912 779.6 0 5912 87 193 779.6 0 193 88 849 779.6 0 849 89 99 779.6 0 99 90 83 779.6 0 83 91 379 779.6 0 379 92 295 779.6 0 295 93 202 779.6 0 202 94 265 779.6 0 265 95 626 779.6 0 626 96 211 779.6 0 211 97 253 779.6 0 253 98 805 779.6 0 805 99 334 779.6 0 334 100 214 779.6 0 214 101 703 779.6 0 703 102 621 779.6 0 621 103 329 779.6 0 329 104 670 779.6 0 670 105 1061 779.6 0 1061 106 227 779.6 0 227 107 440 779.6 0 440 108 835 779.6 0 835 109 319 779.6 0 319 110 404 779.6 0 404 111 699 779.6 0 699 112 447 779.6 0 447 113 616 779.6 0 616 114 959 779.6 0 959 115 673 779.6 0 673 116 984 779.6 0 984 117 2379 779.6 0 2379 118 16401 779.6 0 16401 119 15638 779.6 0 15638 120 31629 779.6 0 31629 121 2808 779.6 0 2808 122 2247 779.6 0 2247 123 4703 779.6 0 4703 124 553 779.6 0 553 125 638 779.6 0 638 126 870 779.6 0 870 127 621 779.6 0 621 128 617 779.6 0 617 129 1042 779.6 0 1042 130 744 779.6 0 744 131 1016 779.6 0 1016 132 1718 779.6 0 1718 133 908 779.6 0 908 134 1148 779.6 0 1148 135 1256 779.6 0 1256 136 1187 779.6 0 1187 137 1163 779.6 0 1163 138 1643 779.6 0 1643 139 6739 779.6 0 6739 140 13234 779.6 0 13234 141 18706 779.6 0 18706 142 19161 779.6 0 19161 143 3142 779.6 0 3142 144 3775 779.6 0 3775 145 52583 779.6 0 52583 146 38386 779.6 0 38386 147 42108 779.6 0 42108 148 6252 779.6 0 6252 149 2602 779.6 0 2602 150 1933 779.6 0 1933 151 1218 779.6 0 1218 152 916 779.6 0 916 153 719 779.6 0 719 154 695 779.6 0 695 155 1300 779.6 0 1300 156 1105 779.6 0 1105 157 1524 779.6 0 1524 158 1150 779.6 0 1150 159 834 779.6 0 834 160 634 779.6 0 634 161 673 779.6 0 673 162 740 779.6 0 740 163 742 779.6 0 742 164 1054 779.6 0 1054 165 4433 779.6 0 4433 166 3800 779.6 0 3800 167 13385 779.6 0 13385 168 1110 779.6 0 1110 169 731 779.6 0 731 170 378 779.6 0 378 171 716 779.6 0 716 172 691 779.6 0 691 173 392 779.6 0 392 174 576 779.6 0 576 175 519 779.6 0 519 176 567 779.6 0 567 177 342 779.6 0 342 178 574 779.6 0 574 179 395 779.6 0 395 180 485 779.6 0 485 181 542 779.6 0 542 182 524 779.6 0 524 183 614 779.6 0 614 184 605 779.6 0 605 185 692 779.6 0 692 186 566 779.6 0 566 187 548 779.6 0 548 188 508 779.6 0 508 189 518 779.6 0 518 190 558 779.6 0 558 191 422 779.6 0 422 192 592 779.6 0 592 193 1021 779.6 0 1021 194 747 779.6 0 747 195 606 779.6 0 606 196 895 779.6 0 895 197 497 779.6 0 497 198 548 779.6 0 548 199 634 779.6 0 634 200 1070 779.6 0 1070 201 678 779.6 0 678 202 410 779.6 0 410 203 365 779.6 0 365 204 555 779.6 0 555 205 672 779.6 0 672 206 434 779.6 0 434 207 447 779.6 0 447 208 517 779.6 0 517 209 447 779.6 0 447 210 537 779.6 0 537 211 427 779.6 0 427 212 520 779.6 0 520 213 546 779.6 0 546 214 430 779.6 0 430 215 463 779.6 0 463 216 551 779.6 0 551 217 580 779.6 0 580 218 742 779.6 0 742 219 898 779.6 0 898 220 448 779.6 0 448 221 558 779.6 0 558 222 397 779.6 0 397 223 265 779.6 0 265 224 387 779.6 0 387 225 289 779.6 0 289 226 391 779.6 0 391 227 347 779.6 0 347 228 348 779.6 0 348 229 416 779.6 0 416 230 408 779.6 0 408 231 371 779.6 0 371 232 468 779.6 0 468 233 539 779.6 0 539 234 335 779.6 0 335 235 404 779.6 0 404 236 561 779.6 0 561 237 530 779.6 0 530 238 505 779.6 0 505 239 566 779.6 0 566 240 544 779.6 0 544 241 470 779.6 0 470 242 431 779.6 0 431 243 301 779.6 0 301 244 370 779.6 0 370 245 363 779.6 0 363 246 843 779.6 0 843 247 884 779.6 0 884 248 1355 779.6 0 1355 249 448 779.6 0 448 250 395 779.6 0 395 251 342 779.6 0 342 252 199 779.6 0 199 253 270 779.6 0 270 254 225 779.6 0 225 255 249 779.6 0 249 256 264 779.6 0 264 257 316 779.6 0 316 258 367 779.6 0 367 259 366 779.6 0 366 260 362 779.6 0 362 261 456 779.6 0 456 262 361 779.6 0 361 263 311 779.6 0 311 264 346 779.6 0 346 265 261 779.6 0 261 266 407 779.6 0 407 267 278 779.6 0 278 268 336 779.6 0 336 269 427 779.6 0 427 270 388 779.6 0 388 271 484 779.6 0 484 272 417 779.6 0 417 273 410 779.6 0 410 274 387 779.6 0 387 275 339 779.6 0 339 276 329 779.6 0 329 277 313 779.6 0 313 278 260 779.6 0 260 279 363 779.6 0 363 280 263 779.6 0 263 281 343 779.6 0 343 282 322 779.6 0 322 283 242 779.6 0 242 284 389 779.6 0 389 285 267 779.6 0 267 286 311 779.6 0 311 287 407 779.6 0 407 288 545 779.6 0 545 289 551 779.6 0 551 290 630 779.6 0 630 291 674 779.6 0 674 292 624 779.6 0 624 293 412 779.6 0 412 294 654 779.6 0 654 295 706 779.6 0 706 296 618 779.6 0 618 297 1193 779.6 0 1193 298 1095 779.6 0 1095 299 713 779.6 0 713 300 504 779.6 0 504 301 1935 779.6 0 1935 Finished in 15.88 s (38 us/read; 1.57 M reads/minute). === Summary === Total reads processed: 414,410 Reads with adapters: 25,090 (6.1%) Reads that were too short: 198 (0.0%) Reads written (passing filters): 24,892 (6.0%) Total basepairs processed: 70,649,030 bp Total written (filtered): 6,552,868 bp (9.3%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 25090 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 14 3 0.0 2 0 0 0 3 15 7 0.0 3 0 0 6 1 16 201 0.0 3 0 192 5 4 17 22515 0.0 3 22099 403 12 1 18 54 0.0 3 5 45 1 3 19 16 0.0 3 4 1 8 3 20 16 0.0 3 0 0 0 16 22 1 0.0 3 0 0 0 1 23 4 0.0 3 0 0 0 4 26 161 0.0 3 0 0 0 161 27 2 0.0 3 0 0 0 2 29 67 0.0 3 0 0 3 64 32 2 0.0 3 0 0 0 2 44 2 0.0 3 0 0 1 1 46 1 0.0 3 0 0 0 1 49 1 0.0 3 0 0 0 1 50 3 0.0 3 0 0 0 3 51 1 0.0 3 0 0 0 1 52 1 0.0 3 0 0 0 1 53 31 0.0 3 0 0 0 31 54 1 0.0 3 0 0 0 1 56 1 0.0 3 0 0 0 1 59 1 0.0 3 0 0 0 1 61 2 0.0 3 0 0 0 2 62 1 0.0 3 0 0 0 1 63 3 0.0 3 0 0 0 3 70 1 0.0 3 0 0 0 1 71 2 0.0 3 0 0 0 2 72 1465 0.0 3 0 0 2 1463 73 18 0.0 3 0 0 0 18 74 149 0.0 3 0 0 0 149 75 1 0.0 3 0 0 0 1 76 39 0.0 3 0 0 0 39 77 22 0.0 3 0 0 0 22 83 2 0.0 3 1 0 0 1 86 1 0.0 3 0 0 0 1 87 2 0.0 3 0 0 0 2 91 1 0.0 3 0 0 0 1 99 3 0.0 3 1 0 0 2 100 1 0.0 3 0 0 0 1 106 29 0.0 3 0 0 0 29 107 20 0.0 3 0 0 0 20 109 1 0.0 3 0 0 0 1 110 34 0.0 3 0 0 0 34 111 2 0.0 3 0 0 0 2 113 3 0.0 3 0 0 0 3 114 3 0.0 3 0 0 0 3 128 15 0.0 3 0 0 1 14 129 2 0.0 3 0 0 0 2 133 1 0.0 3 0 0 0 1 135 5 0.0 3 0 0 0 5 138 40 0.0 3 0 0 0 40 139 1 0.0 3 0 0 0 1 140 11 0.0 3 0 0 0 11 141 73 0.0 3 0 0 0 73 147 1 0.0 3 0 0 0 1 148 5 0.0 3 0 0 0 5 151 2 0.0 3 0 0 0 2 155 1 0.0 3 0 0 0 1 156 1 0.0 3 0 0 0 1 160 1 0.0 3 0 0 0 1 165 3 0.0 3 0 0 0 3 166 2 0.0 3 0 0 1 1 169 1 0.0 3 0 0 0 1 170 1 0.0 3 0 0 0 1 172 1 0.0 3 0 0 0 1 173 1 0.0 3 0 0 0 1 175 2 0.0 3 0 0 0 2 180 2 0.0 3 0 0 0 2 182 1 0.0 3 0 0 0 1 183 2 0.0 3 0 0 0 2 184 1 0.0 3 0 0 0 1 187 1 0.0 3 0 0 0 1 196 4 0.0 3 0 0 1 3 199 2 0.0 3 0 0 0 2 208 2 0.0 3 0 0 0 2 209 6 0.0 3 0 0 0 6 212 1 0.0 3 0 0 0 1 279 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 1.11 s (45 us/read; 1.35 M reads/minute). === Summary === Total reads processed: 24,892 Reads with adapters: 3,520 (14.1%) Reads written (passing filters): 24,892 (100.0%) Total basepairs processed: 6,552,868 bp Total written (filtered): 6,542,285 bp (99.8%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 3520 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 3.8% C: 84.7% G: 10.9% T: 0.6% 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 3497 388.9 0 3497 4 23 97.2 0 23 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.