This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g GTCCGG -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 58.30 s (26 us/read; 2.30 M reads/minute). === Summary === Total reads processed: 2,238,925 Reads with adapters: 459,602 (20.5%) Reads that were too short: 295,472 (13.2%) Reads written (passing filters): 164,130 (7.3%) Total basepairs processed: 673,916,425 bp Total written (filtered): 42,801,946 bp (6.4%) === Adapter 1 === Sequence: GTCCGG; Type: regular 5'; Length: 6; Trimmed: 459602 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 6036 546.6 0 6036 7 54322 546.6 0 54322 8 2015 546.6 0 2015 9 67431 546.6 0 67431 10 102 546.6 0 102 11 55 546.6 0 55 12 24 546.6 0 24 13 28 546.6 0 28 14 19 546.6 0 19 15 22 546.6 0 22 16 16 546.6 0 16 17 31 546.6 0 31 18 24 546.6 0 24 19 18 546.6 0 18 20 19 546.6 0 19 21 22 546.6 0 22 22 17 546.6 0 17 23 22 546.6 0 22 24 17 546.6 0 17 25 26 546.6 0 26 26 23 546.6 0 23 27 17 546.6 0 17 28 16 546.6 0 16 29 19 546.6 0 19 30 29 546.6 0 29 31 180 546.6 0 180 32 91 546.6 0 91 33 41 546.6 0 41 34 54 546.6 0 54 35 71 546.6 0 71 36 29 546.6 0 29 37 41 546.6 0 41 38 30 546.6 0 30 39 31 546.6 0 31 40 21 546.6 0 21 41 49 546.6 0 49 42 30 546.6 0 30 43 37 546.6 0 37 44 27 546.6 0 27 45 23 546.6 0 23 46 20 546.6 0 20 47 19 546.6 0 19 48 22 546.6 0 22 49 21 546.6 0 21 50 25 546.6 0 25 51 20 546.6 0 20 52 23 546.6 0 23 53 29 546.6 0 29 54 42 546.6 0 42 55 40 546.6 0 40 56 27 546.6 0 27 57 53 546.6 0 53 58 36 546.6 0 36 59 34 546.6 0 34 60 275 546.6 0 275 61 24 546.6 0 24 62 25 546.6 0 25 63 12 546.6 0 12 64 20 546.6 0 20 65 57 546.6 0 57 66 57 546.6 0 57 67 45 546.6 0 45 68 14 546.6 0 14 69 20 546.6 0 20 70 21 546.6 0 21 71 36 546.6 0 36 72 23 546.6 0 23 73 28 546.6 0 28 74 23 546.6 0 23 75 63 546.6 0 63 76 76 546.6 0 76 77 144 546.6 0 144 78 48 546.6 0 48 79 19 546.6 0 19 80 20 546.6 0 20 81 29 546.6 0 29 82 27 546.6 0 27 83 17 546.6 0 17 84 24 546.6 0 24 85 29 546.6 0 29 86 21 546.6 0 21 87 26 546.6 0 26 88 18 546.6 0 18 89 40 546.6 0 40 90 34 546.6 0 34 91 42 546.6 0 42 92 34 546.6 0 34 93 67 546.6 0 67 94 30 546.6 0 30 95 41 546.6 0 41 96 30 546.6 0 30 97 25 546.6 0 25 98 25 546.6 0 25 99 36 546.6 0 36 100 44 546.6 0 44 101 32 546.6 0 32 102 38 546.6 0 38 103 61 546.6 0 61 104 44 546.6 0 44 105 31 546.6 0 31 106 46 546.6 0 46 107 34 546.6 0 34 108 32 546.6 0 32 109 28 546.6 0 28 110 42 546.6 0 42 111 63 546.6 0 63 112 67 546.6 0 67 113 709 546.6 0 709 114 1010 546.6 0 1010 115 854 546.6 0 854 116 56 546.6 0 56 117 30 546.6 0 30 118 33 546.6 0 33 119 24 546.6 0 24 120 44 546.6 0 44 121 46 546.6 0 46 122 44 546.6 0 44 123 43 546.6 0 43 124 47 546.6 0 47 125 53 546.6 0 53 126 34 546.6 0 34 127 41 546.6 0 41 128 34 546.6 0 34 129 89 546.6 0 89 130 63 546.6 0 63 131 41 546.6 0 41 132 53 546.6 0 53 133 57 546.6 0 57 134 78 546.6 0 78 135 71 546.6 0 71 136 64 546.6 0 64 137 95 546.6 0 95 138 77 546.6 0 77 139 54 546.6 0 54 140 66 546.6 0 66 141 69 546.6 0 69 142 65 546.6 0 65 143 94 546.6 0 94 144 110 546.6 0 110 145 139 546.6 0 139 146 110 546.6 0 110 147 923 546.6 0 923 148 1493 546.6 0 1493 149 2615 546.6 0 2615 150 415 546.6 0 415 151 39 546.6 0 39 152 42 546.6 0 42 153 51 546.6 0 51 154 54 546.6 0 54 155 67 546.6 0 67 156 74 546.6 0 74 157 63 546.6 0 63 158 68 546.6 0 68 159 45 546.6 0 45 160 55 546.6 0 55 161 82 546.6 0 82 162 67 546.6 0 67 163 63 546.6 0 63 164 51 546.6 0 51 165 49 546.6 0 49 166 38 546.6 0 38 167 48 546.6 0 48 168 50 546.6 0 50 169 134 546.6 0 134 170 112 546.6 0 112 171 44 546.6 0 44 172 59 546.6 0 59 173 49 546.6 0 49 174 123 546.6 0 123 175 82 546.6 0 82 176 77 546.6 0 77 177 62 546.6 0 62 178 62 546.6 0 62 179 78 546.6 0 78 180 81 546.6 0 81 181 114 546.6 0 114 182 102 546.6 0 102 183 121 546.6 0 121 184 107 546.6 0 107 185 131 546.6 0 131 186 168 546.6 0 168 187 250 546.6 0 250 188 198 546.6 0 198 189 970 546.6 0 970 190 550 546.6 0 550 191 1960 546.6 0 1960 192 640 546.6 0 640 193 463 546.6 0 463 194 439 546.6 0 439 195 588 546.6 0 588 196 558 546.6 0 558 197 466 546.6 0 466 198 586 546.6 0 586 199 1380 546.6 0 1380 200 3243 546.6 0 3243 201 5441 546.6 0 5441 202 7644 546.6 0 7644 203 1781 546.6 0 1781 204 1540 546.6 0 1540 205 14525 546.6 0 14525 206 19918 546.6 0 19918 207 43303 546.6 0 43303 208 17718 546.6 0 17718 209 20177 546.6 0 20177 210 14405 546.6 0 14405 211 1945 546.6 0 1945 212 827 546.6 0 827 213 656 546.6 0 656 214 614 546.6 0 614 215 1292 546.6 0 1292 216 774 546.6 0 774 217 501 546.6 0 501 218 988 546.6 0 988 219 1390 546.6 0 1390 220 2114 546.6 0 2114 221 1858 546.6 0 1858 222 1730 546.6 0 1730 223 1473 546.6 0 1473 224 2089 546.6 0 2089 225 7750 546.6 0 7750 226 21732 546.6 0 21732 227 39469 546.6 0 39469 228 19103 546.6 0 19103 229 118 546.6 0 118 230 43 546.6 0 43 231 36 546.6 0 36 232 23 546.6 0 23 233 29 546.6 0 29 234 36 546.6 0 36 235 46 546.6 0 46 236 54 546.6 0 54 237 32 546.6 0 32 238 52 546.6 0 52 239 31 546.6 0 31 240 40 546.6 0 40 241 45 546.6 0 45 242 49 546.6 0 49 243 54 546.6 0 54 244 309 546.6 0 309 245 445 546.6 0 445 246 507 546.6 0 507 247 202 546.6 0 202 248 335 546.6 0 335 249 308 546.6 0 308 250 183 546.6 0 183 251 222 546.6 0 222 252 209 546.6 0 209 253 234 546.6 0 234 254 192 546.6 0 192 255 308 546.6 0 308 256 174 546.6 0 174 257 261 546.6 0 261 258 367 546.6 0 367 259 1186 546.6 0 1186 260 1052 546.6 0 1052 261 1054 546.6 0 1054 262 7900 546.6 0 7900 263 9201 546.6 0 9201 264 17180 546.6 0 17180 265 340 546.6 0 340 266 107 546.6 0 107 267 65 546.6 0 65 268 51 546.6 0 51 269 117 546.6 0 117 270 137 546.6 0 137 271 240 546.6 0 240 272 121 546.6 0 121 273 44 546.6 0 44 274 106 546.6 0 106 275 93 546.6 0 93 276 84 546.6 0 84 277 56 546.6 0 56 278 91 546.6 0 91 279 64 546.6 0 64 280 43 546.6 0 43 281 48 546.6 0 48 282 69 546.6 0 69 283 151 546.6 0 151 284 228 546.6 0 228 285 126 546.6 0 126 286 68 546.6 0 68 287 54 546.6 0 54 288 56 546.6 0 56 289 62 546.6 0 62 290 55 546.6 0 55 291 66 546.6 0 66 292 366 546.6 0 366 293 472 546.6 0 472 294 941 546.6 0 941 295 196 546.6 0 196 296 229 546.6 0 229 297 246 546.6 0 246 298 143 546.6 0 143 299 74 546.6 0 74 300 94 546.6 0 94 301 136 546.6 0 136 Finished in 7.81 s (48 us/read; 1.26 M reads/minute). === Summary === Total reads processed: 164,130 Reads with adapters: 59,533 (36.3%) Reads that were too short: 87 (0.1%) Reads written (passing filters): 59,446 (36.2%) Total basepairs processed: 42,801,946 bp Total written (filtered): 16,254,552 bp (38.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 59533 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 17 7 0.0 3 0 0 0 5 2 18 22 0.0 3 0 0 17 4 1 19 822 0.0 3 0 714 67 26 15 20 57958 0.0 4 54815 2552 432 130 29 21 187 0.0 4 56 113 7 9 2 22 25 0.0 4 10 2 8 4 1 23 69 0.0 4 0 0 0 48 21 24 3 0.0 4 0 0 0 0 3 29 1 0.0 4 0 0 0 0 1 30 1 0.0 4 1 34 1 0.0 4 0 0 0 0 1 36 2 0.0 4 0 0 0 0 2 40 1 0.0 4 0 0 0 0 1 42 1 0.0 4 0 0 0 0 1 44 1 0.0 4 0 1 64 2 0.0 4 0 0 0 0 2 65 1 0.0 4 0 0 0 1 66 1 0.0 4 0 0 0 0 1 68 1 0.0 4 0 0 0 0 1 72 1 0.0 4 0 0 0 0 1 81 1 0.0 4 0 0 1 90 2 0.0 4 0 0 0 0 2 92 1 0.0 4 0 0 0 0 1 102 1 0.0 4 0 0 0 0 1 104 1 0.0 4 0 0 0 0 1 105 3 0.0 4 0 0 0 0 3 109 1 0.0 4 0 0 0 0 1 120 1 0.0 4 0 0 0 0 1 122 1 0.0 4 0 0 0 0 1 126 7 0.0 4 0 0 0 0 7 127 309 0.0 4 0 0 0 0 309 129 1 0.0 4 0 0 0 0 1 130 2 0.0 4 0 0 0 0 2 132 1 0.0 4 0 0 0 0 1 135 19 0.0 4 0 0 0 0 19 136 1 0.0 4 0 0 0 0 1 140 2 0.0 4 0 0 0 0 2 148 1 0.0 4 0 0 0 0 1 152 1 0.0 4 0 0 0 0 1 153 5 0.0 4 0 0 0 1 4 172 1 0.0 4 1 202 1 0.0 4 0 0 0 0 1 203 1 0.0 4 0 0 0 0 1 207 1 0.0 4 0 0 0 0 1 208 1 0.0 4 0 0 0 0 1 220 1 0.0 4 0 0 0 0 1 225 2 0.0 4 0 0 0 0 2 226 1 0.0 4 0 0 0 0 1 227 2 0.0 4 0 0 0 0 2 228 14 0.0 4 0 0 0 1 13 229 15 0.0 4 0 0 0 1 14 230 2 0.0 4 0 0 0 0 2 233 3 0.0 4 0 0 0 0 3 234 1 0.0 4 0 0 0 0 1 235 3 0.0 4 0 0 0 0 3 236 1 0.0 4 0 0 0 0 1 238 2 0.0 4 0 0 0 0 2 255 1 0.0 4 0 0 0 0 1 258 1 0.0 4 0 0 0 0 1 261 1 0.0 4 0 0 0 0 1 262 2 0.0 4 0 0 0 0 2 264 1 0.0 4 0 0 0 0 1 265 1 0.0 4 0 0 0 0 1 274 1 0.0 4 0 0 0 0 1 283 2 0.0 4 0 0 0 0 2 284 1 0.0 4 0 0 0 0 1 290 1 0.0 4 0 0 0 0 1 291 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 2.06 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 59,446 Reads with adapters: 2,431 (4.1%) Reads written (passing filters): 59,446 (100.0%) Total basepairs processed: 16,254,552 bp Total written (filtered): 16,222,505 bp (99.8%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2431 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 8.5% C: 13.7% G: 75.1% T: 2.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 213 928.8 0 213 4 36 232.2 0 36 5 1 58.1 0 1 9 15 0.2 0 1 14 10 46 0.1 1 1 45 11 841 0.0 1 49 792 12 1142 0.0 1 64 1078 13 96 0.0 1 10 86 14 4 0.0 1 1 3 15 1 0.0 1 0 1 16 1 0.0 1 0 1 152 15 0.0 1 9 6 171 2 0.0 1 2 179 1 0.0 1 1 210 14 0.0 1 10 4 211 3 0.0 1 2 1