This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGAGAC -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 70.95 s (26 us/read; 2.29 M reads/minute). === Summary === Total reads processed: 2,708,680 Reads with adapters: 271,249 (10.0%) Reads that were too short: 43,599 (1.6%) Reads written (passing filters): 227,650 (8.4%) Total basepairs processed: 815,312,680 bp Total written (filtered): 48,953,574 bp (6.0%) === Adapter 1 === Sequence: AGAGAC; Type: regular 5'; Length: 6; Trimmed: 271249 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 311 661.3 0 311 7 18709 661.3 0 18709 8 4472 661.3 0 4472 9 9 661.3 0 9 10 137 661.3 0 137 11 7 661.3 0 7 12 105 661.3 0 105 13 49 661.3 0 49 14 6 661.3 0 6 15 3 661.3 0 3 16 9 661.3 0 9 17 6 661.3 0 6 18 5 661.3 0 5 19 5 661.3 0 5 20 7 661.3 0 7 21 6 661.3 0 6 22 10 661.3 0 10 23 7 661.3 0 7 24 7 661.3 0 7 25 12 661.3 0 12 26 7 661.3 0 7 27 11 661.3 0 11 28 26 661.3 0 26 29 17 661.3 0 17 30 20 661.3 0 20 31 14 661.3 0 14 32 15 661.3 0 15 33 13 661.3 0 13 34 13 661.3 0 13 35 20 661.3 0 20 36 23 661.3 0 23 37 12 661.3 0 12 38 35 661.3 0 35 39 8 661.3 0 8 40 15 661.3 0 15 41 9 661.3 0 9 42 27 661.3 0 27 43 36 661.3 0 36 44 11 661.3 0 11 45 17 661.3 0 17 46 13 661.3 0 13 47 31 661.3 0 31 48 26 661.3 0 26 49 44 661.3 0 44 50 20 661.3 0 20 51 45 661.3 0 45 52 228 661.3 0 228 53 86 661.3 0 86 54 39 661.3 0 39 55 24 661.3 0 24 56 21 661.3 0 21 57 138 661.3 0 138 58 12 661.3 0 12 59 45 661.3 0 45 60 31 661.3 0 31 61 130 661.3 0 130 62 340 661.3 0 340 63 65 661.3 0 65 64 196 661.3 0 196 65 108 661.3 0 108 66 278 661.3 0 278 67 487 661.3 0 487 68 151 661.3 0 151 69 120 661.3 0 120 70 56 661.3 0 56 71 240 661.3 0 240 72 182 661.3 0 182 73 362 661.3 0 362 74 493 661.3 0 493 75 717 661.3 0 717 76 1006 661.3 0 1006 77 2116 661.3 0 2116 78 5986 661.3 0 5986 79 86761 661.3 0 86761 80 14284 661.3 0 14284 81 44759 661.3 0 44759 82 353 661.3 0 353 83 201 661.3 0 201 84 92 661.3 0 92 85 65 661.3 0 65 86 70 661.3 0 70 87 46 661.3 0 46 88 44 661.3 0 44 89 20 661.3 0 20 90 44 661.3 0 44 91 72 661.3 0 72 92 46 661.3 0 46 93 149 661.3 0 149 94 99 661.3 0 99 95 128 661.3 0 128 96 124 661.3 0 124 97 96 661.3 0 96 98 105 661.3 0 105 99 124 661.3 0 124 100 145 661.3 0 145 101 291 661.3 0 291 102 222 661.3 0 222 103 121 661.3 0 121 104 71 661.3 0 71 105 55 661.3 0 55 106 42 661.3 0 42 107 57 661.3 0 57 108 59 661.3 0 59 109 123 661.3 0 123 110 124 661.3 0 124 111 179 661.3 0 179 112 123 661.3 0 123 113 145 661.3 0 145 114 121 661.3 0 121 115 200 661.3 0 200 116 481 661.3 0 481 117 706 661.3 0 706 118 639 661.3 0 639 119 263 661.3 0 263 120 200 661.3 0 200 121 285 661.3 0 285 122 289 661.3 0 289 123 337 661.3 0 337 124 269 661.3 0 269 125 220 661.3 0 220 126 201 661.3 0 201 127 185 661.3 0 185 128 188 661.3 0 188 129 263 661.3 0 263 130 677 661.3 0 677 131 359 661.3 0 359 132 470 661.3 0 470 133 273 661.3 0 273 134 274 661.3 0 274 135 252 661.3 0 252 136 334 661.3 0 334 137 425 661.3 0 425 138 380 661.3 0 380 139 334 661.3 0 334 140 318 661.3 0 318 141 379 661.3 0 379 142 482 661.3 0 482 143 318 661.3 0 318 144 322 661.3 0 322 145 357 661.3 0 357 146 412 661.3 0 412 147 497 661.3 0 497 148 457 661.3 0 457 149 393 661.3 0 393 150 604 661.3 0 604 151 4329 661.3 0 4329 152 1539 661.3 0 1539 153 347 661.3 0 347 154 335 661.3 0 335 155 324 661.3 0 324 156 437 661.3 0 437 157 346 661.3 0 346 158 426 661.3 0 426 159 375 661.3 0 375 160 357 661.3 0 357 161 424 661.3 0 424 162 291 661.3 0 291 163 352 661.3 0 352 164 230 661.3 0 230 165 316 661.3 0 316 166 398 661.3 0 398 167 531 661.3 0 531 168 434 661.3 0 434 169 380 661.3 0 380 170 1021 661.3 0 1021 171 703 661.3 0 703 172 978 661.3 0 978 173 462 661.3 0 462 174 553 661.3 0 553 175 333 661.3 0 333 176 409 661.3 0 409 177 345 661.3 0 345 178 351 661.3 0 351 179 405 661.3 0 405 180 299 661.3 0 299 181 361 661.3 0 361 182 367 661.3 0 367 183 371 661.3 0 371 184 386 661.3 0 386 185 397 661.3 0 397 186 499 661.3 0 499 187 663 661.3 0 663 188 600 661.3 0 600 189 357 661.3 0 357 190 328 661.3 0 328 191 346 661.3 0 346 192 368 661.3 0 368 193 368 661.3 0 368 194 452 661.3 0 452 195 386 661.3 0 386 196 451 661.3 0 451 197 334 661.3 0 334 198 565 661.3 0 565 199 666 661.3 0 666 200 328 661.3 0 328 201 357 661.3 0 357 202 255 661.3 0 255 203 343 661.3 0 343 204 415 661.3 0 415 205 436 661.3 0 436 206 415 661.3 0 415 207 344 661.3 0 344 208 345 661.3 0 345 209 382 661.3 0 382 210 339 661.3 0 339 211 378 661.3 0 378 212 461 661.3 0 461 213 462 661.3 0 462 214 429 661.3 0 429 215 408 661.3 0 408 216 399 661.3 0 399 217 643 661.3 0 643 218 517 661.3 0 517 219 621 661.3 0 621 220 448 661.3 0 448 221 508 661.3 0 508 222 523 661.3 0 523 223 503 661.3 0 503 224 506 661.3 0 506 225 429 661.3 0 429 226 354 661.3 0 354 227 407 661.3 0 407 228 513 661.3 0 513 229 353 661.3 0 353 230 333 661.3 0 333 231 331 661.3 0 331 232 396 661.3 0 396 233 337 661.3 0 337 234 340 661.3 0 340 235 359 661.3 0 359 236 416 661.3 0 416 237 399 661.3 0 399 238 523 661.3 0 523 239 532 661.3 0 532 240 525 661.3 0 525 241 427 661.3 0 427 242 437 661.3 0 437 243 453 661.3 0 453 244 382 661.3 0 382 245 381 661.3 0 381 246 342 661.3 0 342 247 394 661.3 0 394 248 405 661.3 0 405 249 463 661.3 0 463 250 326 661.3 0 326 251 491 661.3 0 491 252 329 661.3 0 329 253 504 661.3 0 504 254 377 661.3 0 377 255 364 661.3 0 364 256 340 661.3 0 340 257 343 661.3 0 343 258 310 661.3 0 310 259 300 661.3 0 300 260 346 661.3 0 346 261 426 661.3 0 426 262 442 661.3 0 442 263 522 661.3 0 522 264 446 661.3 0 446 265 394 661.3 0 394 266 315 661.3 0 315 267 370 661.3 0 370 268 336 661.3 0 336 269 450 661.3 0 450 270 314 661.3 0 314 271 533 661.3 0 533 272 526 661.3 0 526 273 578 661.3 0 578 274 442 661.3 0 442 275 492 661.3 0 492 276 441 661.3 0 441 277 442 661.3 0 442 278 402 661.3 0 402 279 352 661.3 0 352 280 470 661.3 0 470 281 375 661.3 0 375 282 422 661.3 0 422 283 283 661.3 0 283 284 391 661.3 0 391 285 320 661.3 0 320 286 289 661.3 0 289 287 378 661.3 0 378 288 413 661.3 0 413 289 534 661.3 0 534 290 634 661.3 0 634 291 920 661.3 0 920 292 631 661.3 0 631 293 554 661.3 0 554 294 450 661.3 0 450 295 446 661.3 0 446 296 499 661.3 0 499 297 742 661.3 0 742 298 783 661.3 0 783 299 764 661.3 0 764 300 588 661.3 0 588 301 149 661.3 0 149 Finished in 8.53 s (37 us/read; 1.60 M reads/minute). === Summary === Total reads processed: 227,650 Reads with adapters: 18,834 (8.3%) Reads that were too short: 47 (0.0%) Reads written (passing filters): 18,787 (8.3%) Total basepairs processed: 48,953,574 bp Total written (filtered): 5,198,235 bp (10.6%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 18834 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 15 5 0.0 3 0 0 4 1 16 158 0.0 3 0 155 3 17 18493 0.0 3 18284 205 4 18 53 0.0 3 2 48 2 1 19 11 0.0 3 0 0 10 1 20 27 0.0 3 2 0 0 25 22 1 0.0 3 0 0 0 1 23 1 0.0 3 0 0 0 1 26 1 0.0 3 0 0 0 1 27 1 0.0 3 0 0 0 1 29 1 0.0 3 1 31 1 0.0 3 0 0 0 1 37 2 0.0 3 0 0 0 2 40 1 0.0 3 0 0 0 1 41 12 0.0 3 0 0 1 11 44 5 0.0 3 0 0 0 5 51 1 0.0 3 0 0 0 1 56 1 0.0 3 0 0 0 1 57 1 0.0 3 0 0 0 1 58 1 0.0 3 0 0 0 1 59 1 0.0 3 0 0 0 1 60 1 0.0 3 0 0 0 1 71 1 0.0 3 0 0 0 1 72 1 0.0 3 0 0 0 1 75 2 0.0 3 0 0 0 2 76 1 0.0 3 0 0 0 1 79 1 0.0 3 0 0 0 1 95 1 0.0 3 0 0 0 1 101 1 0.0 3 0 0 0 1 106 2 0.0 3 0 0 0 2 121 3 0.0 3 0 0 0 3 122 2 0.0 3 0 0 0 2 134 1 0.0 3 0 0 0 1 146 1 0.0 3 0 0 0 1 149 7 0.0 3 0 0 0 7 150 1 0.0 3 0 0 0 1 151 1 0.0 3 0 0 0 1 167 1 0.0 3 0 0 0 1 171 1 0.0 3 0 0 0 1 185 1 0.0 3 0 0 0 1 192 1 0.0 3 0 0 0 1 206 2 0.0 3 0 0 0 2 207 1 0.0 3 0 0 0 1 208 3 0.0 3 0 0 0 3 209 3 0.0 3 0 0 0 3 210 8 0.0 3 0 0 0 8 211 3 0.0 3 0 0 0 3 216 1 0.0 3 0 0 0 1 217 1 0.0 3 0 0 0 1 222 1 0.0 3 0 0 0 1 275 1 0.0 3 0 0 0 1 278 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 0.67 s (36 us/read; 1.68 M reads/minute). === Summary === Total reads processed: 18,787 Reads with adapters: 1,289 (6.9%) Reads written (passing filters): 18,787 (100.0%) Total basepairs processed: 5,198,235 bp Total written (filtered): 5,194,367 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 1289 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 5.3% C: 89.8% G: 4.3% 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 1288 293.5 0 1288 4 1 73.4 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.