This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g ATTCTA -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 90.49 s (26 us/read; 2.30 M reads/minute). === Summary === Total reads processed: 3,465,239 Reads with adapters: 349,085 (10.1%) Reads that were too short: 26,194 (0.8%) Reads written (passing filters): 322,891 (9.3%) Total basepairs processed: 1,043,036,939 bp Total written (filtered): 53,254,105 bp (5.1%) === Adapter 1 === Sequence: ATTCTA; Type: regular 5'; Length: 6; Trimmed: 349085 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 101 846.0 0 101 7 8119 846.0 0 8119 8 8471 846.0 0 8471 9 17 846.0 0 17 10 9 846.0 0 9 11 10 846.0 0 10 12 35 846.0 0 35 13 60 846.0 0 60 14 15 846.0 0 15 15 10 846.0 0 10 16 7 846.0 0 7 17 8 846.0 0 8 18 5 846.0 0 5 19 6 846.0 0 6 20 18 846.0 0 18 21 7 846.0 0 7 22 7 846.0 0 7 23 7 846.0 0 7 24 8 846.0 0 8 25 10 846.0 0 10 26 13 846.0 0 13 27 18 846.0 0 18 28 12 846.0 0 12 29 8 846.0 0 8 30 3 846.0 0 3 31 14 846.0 0 14 32 5 846.0 0 5 33 5 846.0 0 5 34 24 846.0 0 24 35 38 846.0 0 38 36 2 846.0 0 2 37 4 846.0 0 4 38 9 846.0 0 9 39 3 846.0 0 3 40 7 846.0 0 7 41 5 846.0 0 5 42 9 846.0 0 9 43 23 846.0 0 23 44 16 846.0 0 16 45 4 846.0 0 4 46 6 846.0 0 6 47 6 846.0 0 6 48 9 846.0 0 9 49 3 846.0 0 3 50 5 846.0 0 5 51 7 846.0 0 7 52 3 846.0 0 3 53 9 846.0 0 9 54 11 846.0 0 11 55 10 846.0 0 10 56 10 846.0 0 10 57 3 846.0 0 3 58 12 846.0 0 12 59 5 846.0 0 5 60 12 846.0 0 12 61 11 846.0 0 11 62 8 846.0 0 8 63 12 846.0 0 12 64 11 846.0 0 11 65 8 846.0 0 8 66 11 846.0 0 11 67 17 846.0 0 17 68 13 846.0 0 13 69 6 846.0 0 6 70 13 846.0 0 13 71 22 846.0 0 22 72 16 846.0 0 16 73 16 846.0 0 16 74 9 846.0 0 9 75 18 846.0 0 18 76 2 846.0 0 2 77 2 846.0 0 2 78 11 846.0 0 11 79 5 846.0 0 5 80 37 846.0 0 37 81 42 846.0 0 42 82 62 846.0 0 62 83 93 846.0 0 93 84 135 846.0 0 135 85 117 846.0 0 117 86 48 846.0 0 48 87 33 846.0 0 33 88 28 846.0 0 28 89 108 846.0 0 108 90 207 846.0 0 207 91 242 846.0 0 242 92 217 846.0 0 217 93 550 846.0 0 550 94 112 846.0 0 112 95 225 846.0 0 225 96 225 846.0 0 225 97 191 846.0 0 191 98 220 846.0 0 220 99 186 846.0 0 186 100 225 846.0 0 225 101 348 846.0 0 348 102 908 846.0 0 908 103 886 846.0 0 886 104 500 846.0 0 500 105 136 846.0 0 136 106 138 846.0 0 138 107 78 846.0 0 78 108 121 846.0 0 121 109 451 846.0 0 451 110 422 846.0 0 422 111 460 846.0 0 460 112 273 846.0 0 273 113 283 846.0 0 283 114 279 846.0 0 279 115 400 846.0 0 400 116 199 846.0 0 199 117 143 846.0 0 143 118 132 846.0 0 132 119 88 846.0 0 88 120 114 846.0 0 114 121 107 846.0 0 107 122 339 846.0 0 339 123 437 846.0 0 437 124 398 846.0 0 398 125 694 846.0 0 694 126 223 846.0 0 223 127 328 846.0 0 328 128 283 846.0 0 283 129 339 846.0 0 339 130 352 846.0 0 352 131 304 846.0 0 304 132 387 846.0 0 387 133 258 846.0 0 258 134 241 846.0 0 241 135 274 846.0 0 274 136 430 846.0 0 430 137 833 846.0 0 833 138 835 846.0 0 835 139 1378 846.0 0 1378 140 2320 846.0 0 2320 141 2350 846.0 0 2350 142 51917 846.0 0 51917 143 181349 846.0 0 181349 144 23610 846.0 0 23610 145 406 846.0 0 406 146 285 846.0 0 285 147 506 846.0 0 506 148 408 846.0 0 408 149 346 846.0 0 346 150 220 846.0 0 220 151 205 846.0 0 205 152 148 846.0 0 148 153 195 846.0 0 195 154 132 846.0 0 132 155 723 846.0 0 723 156 435 846.0 0 435 157 441 846.0 0 441 158 334 846.0 0 334 159 227 846.0 0 227 160 351 846.0 0 351 161 304 846.0 0 304 162 3515 846.0 0 3515 163 5772 846.0 0 5772 164 1852 846.0 0 1852 165 197 846.0 0 197 166 135 846.0 0 135 167 440 846.0 0 440 168 663 846.0 0 663 169 373 846.0 0 373 170 198 846.0 0 198 171 137 846.0 0 137 172 130 846.0 0 130 173 158 846.0 0 158 174 96 846.0 0 96 175 202 846.0 0 202 176 479 846.0 0 479 177 482 846.0 0 482 178 395 846.0 0 395 179 181 846.0 0 181 180 141 846.0 0 141 181 144 846.0 0 144 182 132 846.0 0 132 183 213 846.0 0 213 184 345 846.0 0 345 185 251 846.0 0 251 186 185 846.0 0 185 187 146 846.0 0 146 188 231 846.0 0 231 189 290 846.0 0 290 190 338 846.0 0 338 191 171 846.0 0 171 192 177 846.0 0 177 193 176 846.0 0 176 194 167 846.0 0 167 195 217 846.0 0 217 196 229 846.0 0 229 197 277 846.0 0 277 198 433 846.0 0 433 199 146 846.0 0 146 200 196 846.0 0 196 201 93 846.0 0 93 202 161 846.0 0 161 203 350 846.0 0 350 204 288 846.0 0 288 205 258 846.0 0 258 206 346 846.0 0 346 207 275 846.0 0 275 208 208 846.0 0 208 209 209 846.0 0 209 210 296 846.0 0 296 211 326 846.0 0 326 212 278 846.0 0 278 213 243 846.0 0 243 214 351 846.0 0 351 215 298 846.0 0 298 216 370 846.0 0 370 217 322 846.0 0 322 218 253 846.0 0 253 219 208 846.0 0 208 220 140 846.0 0 140 221 130 846.0 0 130 222 257 846.0 0 257 223 422 846.0 0 422 224 586 846.0 0 586 225 257 846.0 0 257 226 221 846.0 0 221 227 361 846.0 0 361 228 218 846.0 0 218 229 199 846.0 0 199 230 206 846.0 0 206 231 188 846.0 0 188 232 237 846.0 0 237 233 338 846.0 0 338 234 338 846.0 0 338 235 346 846.0 0 346 236 240 846.0 0 240 237 233 846.0 0 233 238 243 846.0 0 243 239 208 846.0 0 208 240 240 846.0 0 240 241 167 846.0 0 167 242 159 846.0 0 159 243 294 846.0 0 294 244 351 846.0 0 351 245 365 846.0 0 365 246 447 846.0 0 447 247 247 846.0 0 247 248 148 846.0 0 148 249 48 846.0 0 48 250 64 846.0 0 64 251 145 846.0 0 145 252 251 846.0 0 251 253 435 846.0 0 435 254 221 846.0 0 221 255 421 846.0 0 421 256 353 846.0 0 353 257 351 846.0 0 351 258 356 846.0 0 356 259 381 846.0 0 381 260 261 846.0 0 261 261 218 846.0 0 218 262 486 846.0 0 486 263 401 846.0 0 401 264 303 846.0 0 303 265 233 846.0 0 233 266 388 846.0 0 388 267 133 846.0 0 133 268 227 846.0 0 227 269 162 846.0 0 162 270 109 846.0 0 109 271 210 846.0 0 210 272 228 846.0 0 228 273 279 846.0 0 279 274 212 846.0 0 212 275 230 846.0 0 230 276 183 846.0 0 183 277 153 846.0 0 153 278 190 846.0 0 190 279 292 846.0 0 292 280 200 846.0 0 200 281 186 846.0 0 186 282 272 846.0 0 272 283 351 846.0 0 351 284 397 846.0 0 397 285 310 846.0 0 310 286 331 846.0 0 331 287 301 846.0 0 301 288 110 846.0 0 110 289 96 846.0 0 96 290 78 846.0 0 78 291 122 846.0 0 122 292 557 846.0 0 557 293 450 846.0 0 450 294 204 846.0 0 204 295 258 846.0 0 258 296 191 846.0 0 191 297 138 846.0 0 138 298 110 846.0 0 110 299 150 846.0 0 150 300 255 846.0 0 255 301 377 846.0 0 377 Finished in 10.02 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 322,891 Reads with adapters: 8,065 (2.5%) Reads that were too short: 31 (0.0%) Reads written (passing filters): 8,034 (2.5%) Total basepairs processed: 53,254,105 bp Total written (filtered): 2,224,270 bp (4.2%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 8065 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 1 0.0 3 0 0 1 16 35 0.0 3 0 35 17 7949 0.0 3 7876 72 1 18 34 0.0 3 4 26 2 2 19 4 0.0 3 0 0 3 1 20 4 0.0 3 0 0 0 4 24 1 0.0 3 0 0 0 1 36 1 0.0 3 0 0 0 1 45 1 0.0 3 0 0 0 1 50 1 0.0 3 0 0 0 1 58 1 0.0 3 0 0 0 1 69 1 0.0 3 0 0 1 70 1 0.0 3 0 0 0 1 73 1 0.0 3 0 0 1 79 1 0.0 3 0 0 0 1 80 1 0.0 3 0 0 0 1 81 1 0.0 3 0 0 0 1 109 2 0.0 3 0 0 0 2 113 1 0.0 3 0 0 0 1 116 1 0.0 3 0 0 0 1 123 1 0.0 3 0 0 0 1 129 1 0.0 3 0 0 0 1 133 2 0.0 3 0 0 0 2 137 1 0.0 3 0 0 0 1 138 1 0.0 3 0 0 0 1 146 2 0.0 3 0 0 0 2 147 3 0.0 3 0 0 0 3 148 1 0.0 3 0 0 0 1 153 4 0.0 3 0 0 0 4 154 2 0.0 3 0 0 0 2 179 1 0.0 3 0 0 0 1 187 2 0.0 3 0 0 0 2 192 1 0.0 3 0 0 0 1 198 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 0.29 s (36 us/read; 1.66 M reads/minute). === Summary === Total reads processed: 8,034 Reads with adapters: 692 (8.6%) Reads written (passing filters): 8,034 (100.0%) Total basepairs processed: 2,224,270 bp Total written (filtered): 2,222,190 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 692 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 5.6% C: 88.0% G: 5.6% T: 0.7% 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 3 690 125.5 0 690 4 1 31.4 0 1 6 1 2.0 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.