This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AATCCT -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 181.37 s (34 us/read; 1.76 M reads/minute). === Summary === Total reads processed: 5,333,634 Reads with adapters: 777,574 (14.6%) Reads that were too short: 103,516 (1.9%) Reads written (passing filters): 674,058 (12.6%) Total basepairs processed: 1,605,423,834 bp Total written (filtered): 173,499,876 bp (10.8%) === Adapter 1 === Sequence: AATCCT; Type: regular 5'; Length: 6; Trimmed: 777574 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 454 1302.2 0 454 7 9257 1302.2 0 9257 8 299 1302.2 0 299 9 372 1302.2 0 372 10 715 1302.2 0 715 11 1601 1302.2 0 1601 12 71503 1302.2 0 71503 13 1515 1302.2 0 1515 14 286 1302.2 0 286 15 633 1302.2 0 633 16 184 1302.2 0 184 17 191 1302.2 0 191 18 521 1302.2 0 521 19 274 1302.2 0 274 20 348 1302.2 0 348 21 185 1302.2 0 185 22 290 1302.2 0 290 23 764 1302.2 0 764 24 1046 1302.2 0 1046 25 1755 1302.2 0 1755 26 3494 1302.2 0 3494 27 3494 1302.2 0 3494 28 7287 1302.2 0 7287 29 16712 1302.2 0 16712 30 243716 1302.2 0 243716 31 38753 1302.2 0 38753 32 172201 1302.2 0 172201 33 709 1302.2 0 709 34 78 1302.2 0 78 35 34 1302.2 0 34 36 73 1302.2 0 73 37 49 1302.2 0 49 38 7 1302.2 0 7 39 7 1302.2 0 7 40 10 1302.2 0 10 41 6 1302.2 0 6 42 7 1302.2 0 7 43 13 1302.2 0 13 44 19 1302.2 0 19 45 39 1302.2 0 39 46 78 1302.2 0 78 47 28 1302.2 0 28 48 2 1302.2 0 2 49 9 1302.2 0 9 50 4 1302.2 0 4 51 6 1302.2 0 6 52 10 1302.2 0 10 53 7 1302.2 0 7 54 35 1302.2 0 35 55 568 1302.2 0 568 56 51 1302.2 0 51 57 6 1302.2 0 6 58 4 1302.2 0 4 59 3 1302.2 0 3 60 10 1302.2 0 10 61 14 1302.2 0 14 62 6 1302.2 0 6 63 7 1302.2 0 7 64 4 1302.2 0 4 65 5 1302.2 0 5 66 9 1302.2 0 9 67 6 1302.2 0 6 68 4 1302.2 0 4 69 8 1302.2 0 8 70 15 1302.2 0 15 71 18 1302.2 0 18 72 8 1302.2 0 8 73 18 1302.2 0 18 74 14 1302.2 0 14 75 9 1302.2 0 9 76 62 1302.2 0 62 77 267 1302.2 0 267 78 220 1302.2 0 220 79 280 1302.2 0 280 80 431 1302.2 0 431 81 499 1302.2 0 499 82 368 1302.2 0 368 83 468 1302.2 0 468 84 437 1302.2 0 437 85 386 1302.2 0 386 86 215 1302.2 0 215 87 594 1302.2 0 594 88 327 1302.2 0 327 89 572 1302.2 0 572 90 439 1302.2 0 439 91 117 1302.2 0 117 92 160 1302.2 0 160 93 1596 1302.2 0 1596 94 1119 1302.2 0 1119 95 255 1302.2 0 255 96 114 1302.2 0 114 97 287 1302.2 0 287 98 211 1302.2 0 211 99 373 1302.2 0 373 100 2300 1302.2 0 2300 101 1051 1302.2 0 1051 102 1474 1302.2 0 1474 103 1546 1302.2 0 1546 104 2731 1302.2 0 2731 105 1666 1302.2 0 1666 106 2504 1302.2 0 2504 107 675 1302.2 0 675 108 58 1302.2 0 58 109 211 1302.2 0 211 110 811 1302.2 0 811 111 581 1302.2 0 581 112 252 1302.2 0 252 113 271 1302.2 0 271 114 179 1302.2 0 179 115 304 1302.2 0 304 116 302 1302.2 0 302 117 407 1302.2 0 407 118 3287 1302.2 0 3287 119 1822 1302.2 0 1822 120 1313 1302.2 0 1313 121 313 1302.2 0 313 122 450 1302.2 0 450 123 477 1302.2 0 477 124 745 1302.2 0 745 125 872 1302.2 0 872 126 534 1302.2 0 534 127 267 1302.2 0 267 128 224 1302.2 0 224 129 233 1302.2 0 233 130 465 1302.2 0 465 131 1113 1302.2 0 1113 132 948 1302.2 0 948 133 719 1302.2 0 719 134 431 1302.2 0 431 135 573 1302.2 0 573 136 546 1302.2 0 546 137 874 1302.2 0 874 138 1981 1302.2 0 1981 139 948 1302.2 0 948 140 346 1302.2 0 346 141 458 1302.2 0 458 142 702 1302.2 0 702 143 583 1302.2 0 583 144 1210 1302.2 0 1210 145 568 1302.2 0 568 146 548 1302.2 0 548 147 364 1302.2 0 364 148 286 1302.2 0 286 149 830 1302.2 0 830 150 636 1302.2 0 636 151 692 1302.2 0 692 152 426 1302.2 0 426 153 642 1302.2 0 642 154 1443 1302.2 0 1443 155 528 1302.2 0 528 156 529 1302.2 0 529 157 884 1302.2 0 884 158 1037 1302.2 0 1037 159 2401 1302.2 0 2401 160 810 1302.2 0 810 161 1141 1302.2 0 1141 162 670 1302.2 0 670 163 874 1302.2 0 874 164 1776 1302.2 0 1776 165 1685 1302.2 0 1685 166 963 1302.2 0 963 167 801 1302.2 0 801 168 888 1302.2 0 888 169 375 1302.2 0 375 170 425 1302.2 0 425 171 686 1302.2 0 686 172 460 1302.2 0 460 173 495 1302.2 0 495 174 384 1302.2 0 384 175 235 1302.2 0 235 176 196 1302.2 0 196 177 541 1302.2 0 541 178 787 1302.2 0 787 179 1701 1302.2 0 1701 180 1715 1302.2 0 1715 181 807 1302.2 0 807 182 791 1302.2 0 791 183 989 1302.2 0 989 184 1485 1302.2 0 1485 185 790 1302.2 0 790 186 393 1302.2 0 393 187 245 1302.2 0 245 188 641 1302.2 0 641 189 810 1302.2 0 810 190 1722 1302.2 0 1722 191 951 1302.2 0 951 192 565 1302.2 0 565 193 244 1302.2 0 244 194 246 1302.2 0 246 195 435 1302.2 0 435 196 727 1302.2 0 727 197 816 1302.2 0 816 198 629 1302.2 0 629 199 814 1302.2 0 814 200 522 1302.2 0 522 201 593 1302.2 0 593 202 716 1302.2 0 716 203 2116 1302.2 0 2116 204 2491 1302.2 0 2491 205 1450 1302.2 0 1450 206 1473 1302.2 0 1473 207 578 1302.2 0 578 208 234 1302.2 0 234 209 421 1302.2 0 421 210 552 1302.2 0 552 211 578 1302.2 0 578 212 519 1302.2 0 519 213 447 1302.2 0 447 214 576 1302.2 0 576 215 1259 1302.2 0 1259 216 824 1302.2 0 824 217 987 1302.2 0 987 218 1086 1302.2 0 1086 219 505 1302.2 0 505 220 607 1302.2 0 607 221 200 1302.2 0 200 222 424 1302.2 0 424 223 2014 1302.2 0 2014 224 1917 1302.2 0 1917 225 1078 1302.2 0 1078 226 1221 1302.2 0 1221 227 866 1302.2 0 866 228 1013 1302.2 0 1013 229 539 1302.2 0 539 230 477 1302.2 0 477 231 594 1302.2 0 594 232 615 1302.2 0 615 233 778 1302.2 0 778 234 1412 1302.2 0 1412 235 825 1302.2 0 825 236 285 1302.2 0 285 237 128 1302.2 0 128 238 123 1302.2 0 123 239 161 1302.2 0 161 240 241 1302.2 0 241 241 428 1302.2 0 428 242 493 1302.2 0 493 243 1175 1302.2 0 1175 244 1163 1302.2 0 1163 245 977 1302.2 0 977 246 371 1302.2 0 371 247 217 1302.2 0 217 248 110 1302.2 0 110 249 216 1302.2 0 216 250 580 1302.2 0 580 251 1046 1302.2 0 1046 252 1886 1302.2 0 1886 253 2424 1302.2 0 2424 254 5275 1302.2 0 5275 255 2734 1302.2 0 2734 256 2109 1302.2 0 2109 257 818 1302.2 0 818 258 1075 1302.2 0 1075 259 1174 1302.2 0 1174 260 2828 1302.2 0 2828 261 2844 1302.2 0 2844 262 11003 1302.2 0 11003 263 1951 1302.2 0 1951 264 1285 1302.2 0 1285 265 917 1302.2 0 917 266 368 1302.2 0 368 267 176 1302.2 0 176 268 200 1302.2 0 200 269 214 1302.2 0 214 270 332 1302.2 0 332 271 486 1302.2 0 486 272 929 1302.2 0 929 273 1531 1302.2 0 1531 274 746 1302.2 0 746 275 1093 1302.2 0 1093 276 3946 1302.2 0 3946 277 1959 1302.2 0 1959 278 2685 1302.2 0 2685 279 1019 1302.2 0 1019 280 668 1302.2 0 668 281 442 1302.2 0 442 282 741 1302.2 0 741 283 819 1302.2 0 819 284 742 1302.2 0 742 285 558 1302.2 0 558 286 370 1302.2 0 370 287 128 1302.2 0 128 288 74 1302.2 0 74 289 103 1302.2 0 103 290 275 1302.2 0 275 291 1052 1302.2 0 1052 292 766 1302.2 0 766 293 495 1302.2 0 495 294 224 1302.2 0 224 295 74 1302.2 0 74 296 95 1302.2 0 95 297 197 1302.2 0 197 298 295 1302.2 0 295 299 548 1302.2 0 548 300 1184 1302.2 0 1184 301 553 1302.2 0 553 Finished in 39.28 s (58 us/read; 1.03 M reads/minute). === Summary === Total reads processed: 674,058 Reads with adapters: 9,397 (1.4%) Reads that were too short: 42 (0.0%) Reads written (passing filters): 9,355 (1.4%) Total basepairs processed: 173,499,876 bp Total written (filtered): 2,541,426 bp (1.5%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 9397 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 16 2 0.0 3 0 0 0 0 2 17 1 0.0 3 0 0 0 1 18 5 0.0 3 0 0 4 1 19 90 0.0 3 0 89 1 20 9037 0.0 4 8885 143 5 3 1 21 22 0.0 4 1 18 1 0 2 22 2 0.0 4 0 0 2 23 2 0.0 4 0 0 0 0 2 24 2 0.0 4 0 0 0 0 2 30 1 0.0 4 0 0 0 0 1 32 1 0.0 4 0 0 1 36 1 0.0 4 0 0 0 0 1 47 1 0.0 4 0 0 0 0 1 53 1 0.0 4 0 0 0 0 1 58 1 0.0 4 0 0 0 0 1 59 1 0.0 4 0 0 0 0 1 64 1 0.0 4 0 0 0 0 1 65 1 0.0 4 0 0 0 0 1 69 2 0.0 4 0 0 0 1 1 77 3 0.0 4 0 0 0 0 3 79 1 0.0 4 0 0 0 0 1 80 1 0.0 4 0 0 0 0 1 81 1 0.0 4 0 0 0 0 1 84 1 0.0 4 0 0 0 0 1 85 1 0.0 4 0 0 0 0 1 95 1 0.0 4 0 0 0 0 1 96 1 0.0 4 0 0 0 0 1 100 1 0.0 4 0 0 0 0 1 101 1 0.0 4 0 0 0 0 1 103 2 0.0 4 0 0 0 0 2 106 2 0.0 4 0 0 0 0 2 109 3 0.0 4 0 0 0 0 3 110 1 0.0 4 0 0 0 0 1 113 1 0.0 4 0 0 0 0 1 114 1 0.0 4 0 0 0 0 1 118 1 0.0 4 0 0 0 0 1 119 1 0.0 4 0 0 0 0 1 121 1 0.0 4 0 0 0 0 1 122 1 0.0 4 0 0 0 0 1 123 1 0.0 4 0 0 0 0 1 124 165 0.0 4 0 0 0 0 165 126 1 0.0 4 0 0 0 0 1 128 1 0.0 4 0 0 0 0 1 129 3 0.0 4 0 0 0 0 3 130 1 0.0 4 0 0 0 0 1 137 1 0.0 4 0 0 0 0 1 143 2 0.0 4 0 0 0 0 2 147 3 0.0 4 0 0 0 0 3 148 3 0.0 4 0 0 0 0 3 149 1 0.0 4 0 0 0 0 1 150 1 0.0 4 0 0 0 0 1 166 2 0.0 4 0 0 0 0 2 181 1 0.0 4 0 0 0 0 1 193 1 0.0 4 0 0 0 0 1 200 1 0.0 4 1 203 1 0.0 4 1 205 1 0.0 4 0 0 0 0 1 225 2 0.0 4 0 0 0 0 2 259 1 0.0 4 0 0 1 264 1 0.0 4 0 0 0 0 1 272 1 0.0 4 0 0 0 1 279 2 0.0 4 0 0 0 0 2 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 0.40 s (43 us/read; 1.40 M reads/minute). === Summary === Total reads processed: 9,355 Reads with adapters: 171 (1.8%) Reads written (passing filters): 9,355 (100.0%) Total basepairs processed: 2,541,426 bp Total written (filtered): 2,501,050 bp (98.4%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 171 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 2.9% C: 88.9% G: 7.0% T: 0.6% none/other: 0.6% 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 2 146.2 0 2 11 7 0.0 1 0 7 12 6 0.0 1 1 5 215 26 0.0 1 21 5 216 1 0.0 1 1 219 1 0.0 1 1 242 7 0.0 1 7 243 1 0.0 1 1 249 1 0.0 1 1 261 1 0.0 1 1 268 1 0.0 1 1 269 113 0.0 1 109 4 270 3 0.0 1 3 274 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.