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 ... 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 94.29 s (30 us/read; 1.97 M reads/minute). === Summary === Total reads processed: 3,094,653 Reads with adapters: 277,334 (9.0%) Reads that were too short: 33,709 (1.1%) Reads written (passing filters): 243,625 (7.9%) Total basepairs processed: 931,490,553 bp Total written (filtered): 52,735,837 bp (5.7%) === Adapter 1 === Sequence: AGAGAC; Type: regular 5'; Length: 6; Trimmed: 277334 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 51 755.5 0 51 7 1007 755.5 0 1007 8 2519 755.5 0 2519 9 10 755.5 0 10 10 12 755.5 0 12 11 25 755.5 0 25 12 118 755.5 0 118 13 35 755.5 0 35 14 18 755.5 0 18 15 52 755.5 0 52 16 19 755.5 0 19 17 16 755.5 0 16 18 29 755.5 0 29 19 45 755.5 0 45 20 19 755.5 0 19 21 50 755.5 0 50 22 22 755.5 0 22 23 20 755.5 0 20 24 24 755.5 0 24 25 54 755.5 0 54 26 101 755.5 0 101 27 157 755.5 0 157 28 6905 755.5 0 6905 29 46 755.5 0 46 30 46 755.5 0 46 31 16 755.5 0 16 32 18 755.5 0 18 33 28 755.5 0 28 34 8 755.5 0 8 35 29 755.5 0 29 36 27 755.5 0 27 37 8 755.5 0 8 38 6 755.5 0 6 39 18 755.5 0 18 40 9 755.5 0 9 41 5 755.5 0 5 42 31 755.5 0 31 43 37 755.5 0 37 44 18 755.5 0 18 45 22 755.5 0 22 46 23 755.5 0 23 47 13 755.5 0 13 48 21 755.5 0 21 49 42 755.5 0 42 50 26 755.5 0 26 51 31 755.5 0 31 52 320 755.5 0 320 53 33 755.5 0 33 54 10 755.5 0 10 55 15 755.5 0 15 56 4 755.5 0 4 57 17 755.5 0 17 58 9 755.5 0 9 59 38 755.5 0 38 60 29 755.5 0 29 61 138 755.5 0 138 62 469 755.5 0 469 63 72 755.5 0 72 64 105 755.5 0 105 65 87 755.5 0 87 66 134 755.5 0 134 67 411 755.5 0 411 68 165 755.5 0 165 69 155 755.5 0 155 70 68 755.5 0 68 71 75 755.5 0 75 72 224 755.5 0 224 73 250 755.5 0 250 74 406 755.5 0 406 75 718 755.5 0 718 76 644 755.5 0 644 77 2704 755.5 0 2704 78 7869 755.5 0 7869 79 157060 755.5 0 157060 80 13155 755.5 0 13155 81 18806 755.5 0 18806 82 171 755.5 0 171 83 151 755.5 0 151 84 73 755.5 0 73 85 38 755.5 0 38 86 80 755.5 0 80 87 36 755.5 0 36 88 18 755.5 0 18 89 41 755.5 0 41 90 16 755.5 0 16 91 114 755.5 0 114 92 28 755.5 0 28 93 71 755.5 0 71 94 43 755.5 0 43 95 134 755.5 0 134 96 73 755.5 0 73 97 47 755.5 0 47 98 45 755.5 0 45 99 88 755.5 0 88 100 64 755.5 0 64 101 289 755.5 0 289 102 116 755.5 0 116 103 115 755.5 0 115 104 35 755.5 0 35 105 63 755.5 0 63 106 35 755.5 0 35 107 52 755.5 0 52 108 68 755.5 0 68 109 44 755.5 0 44 110 56 755.5 0 56 111 113 755.5 0 113 112 53 755.5 0 53 113 83 755.5 0 83 114 53 755.5 0 53 115 160 755.5 0 160 116 199 755.5 0 199 117 1002 755.5 0 1002 118 523 755.5 0 523 119 300 755.5 0 300 120 235 755.5 0 235 121 191 755.5 0 191 122 224 755.5 0 224 123 194 755.5 0 194 124 365 755.5 0 365 125 201 755.5 0 201 126 172 755.5 0 172 127 186 755.5 0 186 128 140 755.5 0 140 129 205 755.5 0 205 130 537 755.5 0 537 131 237 755.5 0 237 132 746 755.5 0 746 133 173 755.5 0 173 134 208 755.5 0 208 135 197 755.5 0 197 136 208 755.5 0 208 137 259 755.5 0 259 138 266 755.5 0 266 139 257 755.5 0 257 140 163 755.5 0 163 141 227 755.5 0 227 142 227 755.5 0 227 143 212 755.5 0 212 144 171 755.5 0 171 145 179 755.5 0 179 146 320 755.5 0 320 147 171 755.5 0 171 148 210 755.5 0 210 149 412 755.5 0 412 150 261 755.5 0 261 151 244 755.5 0 244 152 505 755.5 0 505 153 515 755.5 0 515 154 275 755.5 0 275 155 193 755.5 0 193 156 310 755.5 0 310 157 272 755.5 0 272 158 321 755.5 0 321 159 317 755.5 0 317 160 220 755.5 0 220 161 341 755.5 0 341 162 231 755.5 0 231 163 322 755.5 0 322 164 191 755.5 0 191 165 238 755.5 0 238 166 236 755.5 0 236 167 301 755.5 0 301 168 327 755.5 0 327 169 223 755.5 0 223 170 374 755.5 0 374 171 184 755.5 0 184 172 539 755.5 0 539 173 171 755.5 0 171 174 425 755.5 0 425 175 170 755.5 0 170 176 245 755.5 0 245 177 193 755.5 0 193 178 227 755.5 0 227 179 282 755.5 0 282 180 240 755.5 0 240 181 338 755.5 0 338 182 283 755.5 0 283 183 256 755.5 0 256 184 263 755.5 0 263 185 254 755.5 0 254 186 338 755.5 0 338 187 314 755.5 0 314 188 844 755.5 0 844 189 220 755.5 0 220 190 216 755.5 0 216 191 156 755.5 0 156 192 267 755.5 0 267 193 187 755.5 0 187 194 262 755.5 0 262 195 210 755.5 0 210 196 256 755.5 0 256 197 204 755.5 0 204 198 726 755.5 0 726 199 449 755.5 0 449 200 295 755.5 0 295 201 185 755.5 0 185 202 198 755.5 0 198 203 224 755.5 0 224 204 281 755.5 0 281 205 270 755.5 0 270 206 331 755.5 0 331 207 226 755.5 0 226 208 268 755.5 0 268 209 187 755.5 0 187 210 225 755.5 0 225 211 281 755.5 0 281 212 321 755.5 0 321 213 405 755.5 0 405 214 416 755.5 0 416 215 306 755.5 0 306 216 340 755.5 0 340 217 339 755.5 0 339 218 355 755.5 0 355 219 293 755.5 0 293 220 318 755.5 0 318 221 325 755.5 0 325 222 474 755.5 0 474 223 349 755.5 0 349 224 426 755.5 0 426 225 303 755.5 0 303 226 303 755.5 0 303 227 266 755.5 0 266 228 311 755.5 0 311 229 223 755.5 0 223 230 235 755.5 0 235 231 245 755.5 0 245 232 304 755.5 0 304 233 254 755.5 0 254 234 258 755.5 0 258 235 262 755.5 0 262 236 297 755.5 0 297 237 254 755.5 0 254 238 335 755.5 0 335 239 512 755.5 0 512 240 393 755.5 0 393 241 363 755.5 0 363 242 336 755.5 0 336 243 396 755.5 0 396 244 286 755.5 0 286 245 291 755.5 0 291 246 172 755.5 0 172 247 218 755.5 0 218 248 258 755.5 0 258 249 387 755.5 0 387 250 250 755.5 0 250 251 472 755.5 0 472 252 365 755.5 0 365 253 371 755.5 0 371 254 262 755.5 0 262 255 236 755.5 0 236 256 209 755.5 0 209 257 213 755.5 0 213 258 248 755.5 0 248 259 246 755.5 0 246 260 224 755.5 0 224 261 255 755.5 0 255 262 303 755.5 0 303 263 373 755.5 0 373 264 350 755.5 0 350 265 293 755.5 0 293 266 235 755.5 0 235 267 283 755.5 0 283 268 256 755.5 0 256 269 342 755.5 0 342 270 250 755.5 0 250 271 363 755.5 0 363 272 429 755.5 0 429 273 415 755.5 0 415 274 324 755.5 0 324 275 353 755.5 0 353 276 355 755.5 0 355 277 510 755.5 0 510 278 328 755.5 0 328 279 296 755.5 0 296 280 433 755.5 0 433 281 302 755.5 0 302 282 311 755.5 0 311 283 242 755.5 0 242 284 285 755.5 0 285 285 246 755.5 0 246 286 241 755.5 0 241 287 236 755.5 0 236 288 266 755.5 0 266 289 509 755.5 0 509 290 849 755.5 0 849 291 834 755.5 0 834 292 1049 755.5 0 1049 293 467 755.5 0 467 294 315 755.5 0 315 295 384 755.5 0 384 296 294 755.5 0 294 297 567 755.5 0 567 298 624 755.5 0 624 299 529 755.5 0 529 300 524 755.5 0 524 301 173 755.5 0 173 Finished in 11.82 s (49 us/read; 1.24 M reads/minute). === Summary === Total reads processed: 243,625 Reads with adapters: 3,555 (1.5%) Reads that were too short: 12 (0.0%) Reads written (passing filters): 3,543 (1.5%) Total basepairs processed: 52,735,837 bp Total written (filtered): 965,909 bp (1.8%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 3555 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 18 1 0.0 3 0 0 0 0 1 19 36 0.0 3 0 32 2 0 2 20 2574 0.0 4 2535 25 4 1 9 21 11 0.0 4 3 8 22 907 0.0 4 897 9 0 0 1 23 7 0.0 4 0 4 1 0 2 24 2 0.0 4 1 0 0 0 1 36 1 0.0 4 1 39 1 0.0 4 0 0 0 0 1 42 1 0.0 4 1 58 2 0.0 4 2 60 1 0.0 4 1 76 1 0.0 4 0 0 0 0 1 81 1 0.0 4 0 0 0 0 1 85 1 0.0 4 0 0 0 0 1 87 1 0.0 4 0 0 0 0 1 88 1 0.0 4 0 0 0 0 1 101 1 0.0 4 0 0 0 0 1 136 1 0.0 4 0 0 0 0 1 137 1 0.0 4 0 0 0 0 1 231 1 0.0 4 0 0 0 0 1 242 1 0.0 4 0 0 0 0 1 262 1 0.0 4 0 0 0 0 1 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 0.15 s (42 us/read; 1.42 M reads/minute). === Summary === Total reads processed: 3,543 Reads with adapters: 2,567 (72.5%) Reads written (passing filters): 3,543 (100.0%) Total basepairs processed: 965,909 bp Total written (filtered): 302,561 bp (31.3%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2567 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 85.4% C: 13.8% G: 0.6% T: 0.2% none/other: 0.0% WARNING: The adapter is preceded by "A" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "A" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 9 1 0.0 0 0 1 10 3 0.0 1 0 3 11 8 0.0 1 0 8 231 3 0.0 1 3 232 1 0.0 1 1 243 1 0.0 1 1 256 1 0.0 1 0 1 258 6 0.0 1 6 259 2068 0.0 1 2004 64 260 99 0.0 1 89 10 261 17 0.0 1 15 2 262 2 0.0 1 1 1 263 335 0.0 1 315 20 264 17 0.0 1 16 1 265 1 0.0 1 1 268 3 0.0 1 2 1 274 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.