This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGGATG -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 96.21 s (28 us/read; 2.16 M reads/minute). === Summary === Total reads processed: 3,465,239 Reads with adapters: 675,793 (19.5%) Reads that were too short: 14,790 (0.4%) Reads written (passing filters): 661,003 (19.1%) Total basepairs processed: 1,043,036,939 bp Total written (filtered): 182,124,771 bp (17.5%) === Adapter 1 === Sequence: AGGATG; Type: regular 5'; Length: 6; Trimmed: 675793 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 3597 846.0 0 3597 7 11865 846.0 0 11865 8 546274 846.0 0 546274 9 732 846.0 0 732 10 53 846.0 0 53 11 34 846.0 0 34 12 24 846.0 0 24 13 16 846.0 0 16 14 20 846.0 0 20 15 23 846.0 0 23 16 24 846.0 0 24 17 21 846.0 0 21 18 35 846.0 0 35 19 22 846.0 0 22 20 21 846.0 0 21 21 20 846.0 0 20 22 27 846.0 0 27 23 29 846.0 0 29 24 31 846.0 0 31 25 15 846.0 0 15 26 24 846.0 0 24 27 28 846.0 0 28 28 21 846.0 0 21 29 23 846.0 0 23 30 19 846.0 0 19 31 13 846.0 0 13 32 40 846.0 0 40 33 20 846.0 0 20 34 35 846.0 0 35 35 32 846.0 0 32 36 38 846.0 0 38 37 24 846.0 0 24 38 32 846.0 0 32 39 30 846.0 0 30 40 32 846.0 0 32 41 27 846.0 0 27 42 24 846.0 0 24 43 33 846.0 0 33 44 29 846.0 0 29 45 34 846.0 0 34 46 20 846.0 0 20 47 29 846.0 0 29 48 44 846.0 0 44 49 67 846.0 0 67 50 88 846.0 0 88 51 53 846.0 0 53 52 31 846.0 0 31 53 24 846.0 0 24 54 31 846.0 0 31 55 31 846.0 0 31 56 66 846.0 0 66 57 32 846.0 0 32 58 45 846.0 0 45 59 27 846.0 0 27 60 52 846.0 0 52 61 31 846.0 0 31 62 58 846.0 0 58 63 61 846.0 0 61 64 74 846.0 0 74 65 106 846.0 0 106 66 236 846.0 0 236 67 474 846.0 0 474 68 112 846.0 0 112 69 159 846.0 0 159 70 259 846.0 0 259 71 224 846.0 0 224 72 133 846.0 0 133 73 242 846.0 0 242 74 171 846.0 0 171 75 239 846.0 0 239 76 191 846.0 0 191 77 258 846.0 0 258 78 376 846.0 0 376 79 862 846.0 0 862 80 12746 846.0 0 12746 81 15303 846.0 0 15303 82 17891 846.0 0 17891 83 110 846.0 0 110 84 31 846.0 0 31 85 25 846.0 0 25 86 24 846.0 0 24 87 26 846.0 0 26 88 28 846.0 0 28 89 29 846.0 0 29 90 23 846.0 0 23 91 26 846.0 0 26 92 27 846.0 0 27 93 34 846.0 0 34 94 65 846.0 0 65 95 271 846.0 0 271 96 87 846.0 0 87 97 130 846.0 0 130 98 68 846.0 0 68 99 38 846.0 0 38 100 51 846.0 0 51 101 69 846.0 0 69 102 25 846.0 0 25 103 27 846.0 0 27 104 11 846.0 0 11 105 19 846.0 0 19 106 32 846.0 0 32 107 14 846.0 0 14 108 24 846.0 0 24 109 20 846.0 0 20 110 50 846.0 0 50 111 41 846.0 0 41 112 28 846.0 0 28 113 36 846.0 0 36 114 32 846.0 0 32 115 23 846.0 0 23 116 41 846.0 0 41 117 85 846.0 0 85 118 73 846.0 0 73 119 118 846.0 0 118 120 185 846.0 0 185 121 104 846.0 0 104 122 92 846.0 0 92 123 57 846.0 0 57 124 41 846.0 0 41 125 72 846.0 0 72 126 58 846.0 0 58 127 55 846.0 0 55 128 91 846.0 0 91 129 254 846.0 0 254 130 58 846.0 0 58 131 94 846.0 0 94 132 98 846.0 0 98 133 97 846.0 0 97 134 101 846.0 0 101 135 76 846.0 0 76 136 75 846.0 0 75 137 54 846.0 0 54 138 67 846.0 0 67 139 118 846.0 0 118 140 110 846.0 0 110 141 67 846.0 0 67 142 168 846.0 0 168 143 172 846.0 0 172 144 63 846.0 0 63 145 105 846.0 0 105 146 108 846.0 0 108 147 187 846.0 0 187 148 4949 846.0 0 4949 149 153 846.0 0 153 150 233 846.0 0 233 151 44 846.0 0 44 152 52 846.0 0 52 153 57 846.0 0 57 154 56 846.0 0 56 155 88 846.0 0 88 156 63 846.0 0 63 157 60 846.0 0 60 158 56 846.0 0 56 159 67 846.0 0 67 160 56 846.0 0 56 161 64 846.0 0 64 162 61 846.0 0 61 163 56 846.0 0 56 164 67 846.0 0 67 165 67 846.0 0 67 166 86 846.0 0 86 167 117 846.0 0 117 168 115 846.0 0 115 169 89 846.0 0 89 170 81 846.0 0 81 171 128 846.0 0 128 172 91 846.0 0 91 173 116 846.0 0 116 174 245 846.0 0 245 175 402 846.0 0 402 176 136 846.0 0 136 177 168 846.0 0 168 178 249 846.0 0 249 179 140 846.0 0 140 180 147 846.0 0 147 181 217 846.0 0 217 182 182 846.0 0 182 183 202 846.0 0 202 184 185 846.0 0 185 185 241 846.0 0 241 186 311 846.0 0 311 187 383 846.0 0 383 188 1600 846.0 0 1600 189 7966 846.0 0 7966 190 18172 846.0 0 18172 191 1157 846.0 0 1157 192 235 846.0 0 235 193 261 846.0 0 261 194 300 846.0 0 300 195 1524 846.0 0 1524 196 184 846.0 0 184 197 58 846.0 0 58 198 49 846.0 0 49 199 73 846.0 0 73 200 113 846.0 0 113 201 56 846.0 0 56 202 43 846.0 0 43 203 104 846.0 0 104 204 104 846.0 0 104 205 176 846.0 0 176 206 452 846.0 0 452 207 505 846.0 0 505 208 746 846.0 0 746 209 109 846.0 0 109 210 103 846.0 0 103 211 514 846.0 0 514 212 295 846.0 0 295 213 227 846.0 0 227 214 116 846.0 0 116 215 71 846.0 0 71 216 61 846.0 0 61 217 72 846.0 0 72 218 59 846.0 0 59 219 67 846.0 0 67 220 66 846.0 0 66 221 147 846.0 0 147 222 88 846.0 0 88 223 64 846.0 0 64 224 70 846.0 0 70 225 81 846.0 0 81 226 58 846.0 0 58 227 81 846.0 0 81 228 81 846.0 0 81 229 80 846.0 0 80 230 121 846.0 0 121 231 76 846.0 0 76 232 78 846.0 0 78 233 103 846.0 0 103 234 83 846.0 0 83 235 93 846.0 0 93 236 110 846.0 0 110 237 140 846.0 0 140 238 86 846.0 0 86 239 94 846.0 0 94 240 112 846.0 0 112 241 102 846.0 0 102 242 58 846.0 0 58 243 76 846.0 0 76 244 66 846.0 0 66 245 65 846.0 0 65 246 84 846.0 0 84 247 41 846.0 0 41 248 115 846.0 0 115 249 68 846.0 0 68 250 55 846.0 0 55 251 75 846.0 0 75 252 122 846.0 0 122 253 133 846.0 0 133 254 56 846.0 0 56 255 131 846.0 0 131 256 112 846.0 0 112 257 96 846.0 0 96 258 90 846.0 0 90 259 70 846.0 0 70 260 65 846.0 0 65 261 67 846.0 0 67 262 99 846.0 0 99 263 93 846.0 0 93 264 75 846.0 0 75 265 55 846.0 0 55 266 69 846.0 0 69 267 63 846.0 0 63 268 134 846.0 0 134 269 127 846.0 0 127 270 118 846.0 0 118 271 409 846.0 0 409 272 942 846.0 0 942 273 1200 846.0 0 1200 274 126 846.0 0 126 275 55 846.0 0 55 276 57 846.0 0 57 277 79 846.0 0 79 278 64 846.0 0 64 279 61 846.0 0 61 280 72 846.0 0 72 281 212 846.0 0 212 282 130 846.0 0 130 283 199 846.0 0 199 284 540 846.0 0 540 285 56 846.0 0 56 286 45 846.0 0 45 287 62 846.0 0 62 288 77 846.0 0 77 289 85 846.0 0 85 290 75 846.0 0 75 291 156 846.0 0 156 292 461 846.0 0 461 293 337 846.0 0 337 294 249 846.0 0 249 295 131 846.0 0 131 296 67 846.0 0 67 297 95 846.0 0 95 298 133 846.0 0 133 299 115 846.0 0 115 300 149 846.0 0 149 301 35 846.0 0 35 Finished in 27.24 s (41 us/read; 1.46 M reads/minute). === Summary === Total reads processed: 661,003 Reads with adapters: 555,559 (84.0%) Reads that were too short: 30 (0.0%) Reads written (passing filters): 555,529 (84.0%) Total basepairs processed: 182,124,771 bp Total written (filtered): 151,670,339 bp (83.3%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 555559 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 1 0.0 3 0 0 0 0 1 17 15 0.0 3 0 0 0 5 10 18 194 0.0 3 0 0 183 11 19 4681 0.0 3 0 4580 67 24 10 20 548939 0.0 4 542418 6276 207 25 13 21 1342 0.0 4 302 1021 17 1 1 22 77 0.0 4 8 3 58 5 3 23 216 0.0 4 5 1 5 185 20 24 30 0.0 4 3 2 0 1 24 25 4 0.0 4 3 0 0 1 26 2 0.0 4 2 27 4 0.0 4 2 0 1 1 28 1 0.0 4 1 29 1 0.0 4 1 30 1 0.0 4 1 31 1 0.0 4 1 32 2 0.0 4 2 39 3 0.0 4 1 0 0 0 2 43 1 0.0 4 1 44 1 0.0 4 0 0 0 0 1 45 1 0.0 4 1 46 1 0.0 4 0 0 0 0 1 55 2 0.0 4 0 0 0 0 2 74 1 0.0 4 0 0 0 0 1 82 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 97 1 0.0 4 0 0 0 0 1 108 1 0.0 4 0 0 0 0 1 116 1 0.0 4 0 0 0 0 1 117 1 0.0 4 0 0 0 0 1 128 1 0.0 4 0 0 0 0 1 130 1 0.0 4 0 0 0 0 1 131 1 0.0 4 0 0 0 0 1 135 3 0.0 4 0 0 0 0 3 155 14 0.0 4 0 0 0 0 14 156 1 0.0 4 0 0 0 0 1 157 1 0.0 4 0 0 0 0 1 158 1 0.0 4 0 0 0 0 1 166 1 0.0 4 0 0 0 0 1 175 1 0.0 4 0 0 0 0 1 176 1 0.0 4 0 0 0 0 1 209 1 0.0 4 0 0 0 0 1 211 2 0.0 4 0 0 0 0 2 212 1 0.0 4 0 0 0 0 1 228 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 19.07 s (34 us/read; 1.75 M reads/minute). === Summary === Total reads processed: 555,529 Reads with adapters: 43,877 (7.9%) Reads written (passing filters): 555,529 (100.0%) Total basepairs processed: 151,670,339 bp Total written (filtered): 143,566,970 bp (94.7%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 43877 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 24.2% C: 16.3% G: 45.2% T: 14.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 42 8680.1 0 42 4 44 2170.0 0 44 5 23 542.5 0 23 6 5 135.6 0 5 8 1 8.5 0 1 9 9 2.1 0 1 8 10 1407 0.5 1 61 1346 11 12664 0.1 1 88 12576 12 11 0.0 1 0 11 13 1 0.0 1 1 14 19 0.0 1 0 19 72 1 0.0 1 1 74 1 0.0 1 1 80 2 0.0 1 0 2 141 1 0.0 1 1 151 4 0.0 1 0 4 158 1 0.0 1 1 159 1 0.0 1 1 170 9 0.0 1 9 171 1 0.0 1 1 209 1 0.0 1 0 1 224 1 0.0 1 1 236 1 0.0 1 1 255 11 0.0 1 11 256 1803 0.0 1 1720 83 257 28 0.0 1 28 258 13 0.0 1 13 260 2 0.0 1 2 261 2 0.0 1 2 262 28 0.0 1 27 1 263 5990 0.0 1 5597 393 264 1951 0.0 1 1870 81 265 52 0.0 1 48 4 266 10 0.0 1 10 267 2 0.0 1 2 268 16 0.0 1 16 269 5 0.0 1 4 1 270 92 0.0 1 88 4 271 13269 0.0 1 12792 477 272 6165 0.0 1 5877 288 273 163 0.0 1 156 7 274 25 0.0 1 24 1