This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CACTCT -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 172.43 s (50 us/read; 1.21 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 454,839 (13.1%) Reads that were too short: 19,503 (0.6%) Reads written (passing filters): 435,336 (12.5%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 75,149,416 bp (7.2%) === Adapter 1 === Sequence: CACTCT; Type: regular 5'; Length: 6; Trimmed: 454839 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1902 847.3 0 1902 7 41511 847.3 0 41511 8 311 847.3 0 311 9 28400 847.3 0 28400 10 36 847.3 0 36 11 28 847.3 0 28 12 35 847.3 0 35 13 20 847.3 0 20 14 23 847.3 0 23 15 22 847.3 0 22 16 33 847.3 0 33 17 43 847.3 0 43 18 26 847.3 0 26 19 24 847.3 0 24 20 27 847.3 0 27 21 15 847.3 0 15 22 26 847.3 0 26 23 31 847.3 0 31 24 32 847.3 0 32 25 39 847.3 0 39 26 27 847.3 0 27 27 24 847.3 0 24 28 33 847.3 0 33 29 29 847.3 0 29 30 29 847.3 0 29 31 37 847.3 0 37 32 24 847.3 0 24 33 33 847.3 0 33 34 35 847.3 0 35 35 51 847.3 0 51 36 47 847.3 0 47 37 40 847.3 0 40 38 23 847.3 0 23 39 41 847.3 0 41 40 29 847.3 0 29 41 26 847.3 0 26 42 26 847.3 0 26 43 48 847.3 0 48 44 44 847.3 0 44 45 18 847.3 0 18 46 99 847.3 0 99 47 122 847.3 0 122 48 242 847.3 0 242 49 58 847.3 0 58 50 36 847.3 0 36 51 30 847.3 0 30 52 22 847.3 0 22 53 42 847.3 0 42 54 82 847.3 0 82 55 54 847.3 0 54 56 43 847.3 0 43 57 30 847.3 0 30 58 38 847.3 0 38 59 35 847.3 0 35 60 30 847.3 0 30 61 35 847.3 0 35 62 38 847.3 0 38 63 35 847.3 0 35 64 40 847.3 0 40 65 29 847.3 0 29 66 30 847.3 0 30 67 25 847.3 0 25 68 48 847.3 0 48 69 49 847.3 0 49 70 88 847.3 0 88 71 64 847.3 0 64 72 83 847.3 0 83 73 44 847.3 0 44 74 35 847.3 0 35 75 36 847.3 0 36 76 25 847.3 0 25 77 31 847.3 0 31 78 27 847.3 0 27 79 37 847.3 0 37 80 36 847.3 0 36 81 45 847.3 0 45 82 38 847.3 0 38 83 45 847.3 0 45 84 59 847.3 0 59 85 61 847.3 0 61 86 43 847.3 0 43 87 71 847.3 0 71 88 96 847.3 0 96 89 79 847.3 0 79 90 109 847.3 0 109 91 114 847.3 0 114 92 77 847.3 0 77 93 69 847.3 0 69 94 110 847.3 0 110 95 113 847.3 0 113 96 98 847.3 0 98 97 58 847.3 0 58 98 58 847.3 0 58 99 54 847.3 0 54 100 51 847.3 0 51 101 36 847.3 0 36 102 47 847.3 0 47 103 60 847.3 0 60 104 296 847.3 0 296 105 432 847.3 0 432 106 718 847.3 0 718 107 147 847.3 0 147 108 88 847.3 0 88 109 148 847.3 0 148 110 149 847.3 0 149 111 106 847.3 0 106 112 219 847.3 0 219 113 147 847.3 0 147 114 176 847.3 0 176 115 67 847.3 0 67 116 136 847.3 0 136 117 80 847.3 0 80 118 124 847.3 0 124 119 448 847.3 0 448 120 58 847.3 0 58 121 81 847.3 0 81 122 57 847.3 0 57 123 65 847.3 0 65 124 118 847.3 0 118 125 114 847.3 0 114 126 268 847.3 0 268 127 295 847.3 0 295 128 426 847.3 0 426 129 791 847.3 0 791 130 139 847.3 0 139 131 361 847.3 0 361 132 213 847.3 0 213 133 374 847.3 0 374 134 1428 847.3 0 1428 135 747 847.3 0 747 136 567 847.3 0 567 137 175 847.3 0 175 138 220 847.3 0 220 139 533 847.3 0 533 140 459 847.3 0 459 141 838 847.3 0 838 142 1249 847.3 0 1249 143 1309 847.3 0 1309 144 2749 847.3 0 2749 145 3108 847.3 0 3108 146 41295 847.3 0 41295 147 43820 847.3 0 43820 148 88580 847.3 0 88580 149 1200 847.3 0 1200 150 602 847.3 0 602 151 706 847.3 0 706 152 580 847.3 0 580 153 779 847.3 0 779 154 529 847.3 0 529 155 598 847.3 0 598 156 712 847.3 0 712 157 1196 847.3 0 1196 158 1201 847.3 0 1201 159 2391 847.3 0 2391 160 2956 847.3 0 2956 161 29726 847.3 0 29726 162 45831 847.3 0 45831 163 70743 847.3 0 70743 164 361 847.3 0 361 165 134 847.3 0 134 166 72 847.3 0 72 167 94 847.3 0 94 168 58 847.3 0 58 169 81 847.3 0 81 170 38 847.3 0 38 171 58 847.3 0 58 172 51 847.3 0 51 173 75 847.3 0 75 174 108 847.3 0 108 175 131 847.3 0 131 176 123 847.3 0 123 177 70 847.3 0 70 178 49 847.3 0 49 179 87 847.3 0 87 180 77 847.3 0 77 181 476 847.3 0 476 182 927 847.3 0 927 183 324 847.3 0 324 184 192 847.3 0 192 185 71 847.3 0 71 186 83 847.3 0 83 187 96 847.3 0 96 188 99 847.3 0 99 189 95 847.3 0 95 190 55 847.3 0 55 191 54 847.3 0 54 192 73 847.3 0 73 193 64 847.3 0 64 194 90 847.3 0 90 195 200 847.3 0 200 196 84 847.3 0 84 197 91 847.3 0 91 198 66 847.3 0 66 199 67 847.3 0 67 200 79 847.3 0 79 201 78 847.3 0 78 202 71 847.3 0 71 203 45 847.3 0 45 204 65 847.3 0 65 205 62 847.3 0 62 206 62 847.3 0 62 207 65 847.3 0 65 208 56 847.3 0 56 209 58 847.3 0 58 210 64 847.3 0 64 211 51 847.3 0 51 212 50 847.3 0 50 213 68 847.3 0 68 214 117 847.3 0 117 215 119 847.3 0 119 216 113 847.3 0 113 217 88 847.3 0 88 218 93 847.3 0 93 219 109 847.3 0 109 220 128 847.3 0 128 221 105 847.3 0 105 222 95 847.3 0 95 223 81 847.3 0 81 224 64 847.3 0 64 225 63 847.3 0 63 226 70 847.3 0 70 227 63 847.3 0 63 228 99 847.3 0 99 229 99 847.3 0 99 230 95 847.3 0 95 231 123 847.3 0 123 232 119 847.3 0 119 233 108 847.3 0 108 234 94 847.3 0 94 235 92 847.3 0 92 236 90 847.3 0 90 237 98 847.3 0 98 238 160 847.3 0 160 239 310 847.3 0 310 240 756 847.3 0 756 241 1679 847.3 0 1679 242 1415 847.3 0 1415 243 255 847.3 0 255 244 197 847.3 0 197 245 150 847.3 0 150 246 76 847.3 0 76 247 86 847.3 0 86 248 108 847.3 0 108 249 102 847.3 0 102 250 98 847.3 0 98 251 89 847.3 0 89 252 78 847.3 0 78 253 114 847.3 0 114 254 123 847.3 0 123 255 125 847.3 0 125 256 98 847.3 0 98 257 94 847.3 0 94 258 75 847.3 0 75 259 113 847.3 0 113 260 99 847.3 0 99 261 87 847.3 0 87 262 80 847.3 0 80 263 91 847.3 0 91 264 68 847.3 0 68 265 104 847.3 0 104 266 103 847.3 0 103 267 348 847.3 0 348 268 537 847.3 0 537 269 777 847.3 0 777 270 507 847.3 0 507 271 186 847.3 0 186 272 218 847.3 0 218 273 174 847.3 0 174 274 154 847.3 0 154 275 352 847.3 0 352 276 346 847.3 0 346 277 622 847.3 0 622 278 1016 847.3 0 1016 279 916 847.3 0 916 280 639 847.3 0 639 281 246 847.3 0 246 282 192 847.3 0 192 283 166 847.3 0 166 284 110 847.3 0 110 285 73 847.3 0 73 286 117 847.3 0 117 287 99 847.3 0 99 288 173 847.3 0 173 289 157 847.3 0 157 290 148 847.3 0 148 291 110 847.3 0 110 292 135 847.3 0 135 293 131 847.3 0 131 294 180 847.3 0 180 295 164 847.3 0 164 296 117 847.3 0 117 297 87 847.3 0 87 298 87 847.3 0 87 299 74 847.3 0 74 300 66 847.3 0 66 301 104 847.3 0 104 Finished in 24.35 s (56 us/read; 1.07 M reads/minute). === Summary === Total reads processed: 435,336 Reads with adapters: 29,112 (6.7%) Reads that were too short: 71 (0.0%) Reads written (passing filters): 29,041 (6.7%) Total basepairs processed: 75,149,416 bp Total written (filtered): 7,978,672 bp (10.6%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 29112 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 10 0.0 3 0 0 9 1 16 305 0.0 3 0 302 3 17 28582 0.0 3 28051 515 15 1 18 64 0.0 3 2 59 2 1 19 22 0.0 3 0 0 21 1 20 6 0.0 3 1 0 0 5 22 1 0.0 3 0 0 0 1 24 1 0.0 3 0 0 0 1 28 2 0.0 3 0 0 0 2 29 1 0.0 3 0 0 0 1 40 1 0.0 3 0 0 0 1 44 2 0.0 3 0 1 0 1 46 5 0.0 3 0 0 0 5 47 3 0.0 3 1 0 1 1 48 2 0.0 3 0 1 0 1 50 1 0.0 3 0 0 0 1 51 1 0.0 3 0 0 0 1 52 4 0.0 3 1 0 0 3 53 2 0.0 3 0 0 0 2 55 12 0.0 3 0 0 0 12 56 1 0.0 3 0 0 0 1 63 2 0.0 3 0 0 0 2 65 2 0.0 3 0 0 0 2 67 2 0.0 3 0 0 0 2 68 1 0.0 3 0 0 0 1 69 1 0.0 3 0 0 0 1 71 1 0.0 3 0 0 0 1 73 2 0.0 3 0 0 1 1 87 19 0.0 3 0 0 0 19 88 1 0.0 3 0 0 0 1 90 2 0.0 3 0 0 0 2 106 1 0.0 3 0 0 0 1 112 1 0.0 3 0 0 0 1 119 1 0.0 3 0 0 0 1 124 1 0.0 3 0 0 0 1 125 1 0.0 3 0 0 0 1 127 8 0.0 3 0 0 0 8 128 2 0.0 3 0 0 1 1 129 1 0.0 3 0 0 0 1 131 4 0.0 3 0 0 0 4 132 2 0.0 3 0 0 0 2 136 3 0.0 3 0 0 0 3 139 2 0.0 3 0 0 0 2 141 4 0.0 3 0 0 0 4 142 5 0.0 3 0 0 0 5 143 1 0.0 3 0 0 0 1 147 1 0.0 3 0 0 0 1 148 1 0.0 3 0 0 0 1 172 2 0.0 3 0 0 0 2 175 1 0.0 3 0 0 0 1 185 1 0.0 3 0 0 0 1 187 2 0.0 3 0 0 0 2 188 1 0.0 3 0 0 0 1 192 1 0.0 3 0 0 0 1 202 1 0.0 3 0 0 0 1 248 1 0.0 3 0 0 0 1 281 1 0.0 3 0 0 0 1 282 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 1.74 s (60 us/read; 1.00 M reads/minute). === Summary === Total reads processed: 29,041 Reads with adapters: 859 (3.0%) Reads written (passing filters): 29,041 (100.0%) Total basepairs processed: 7,978,672 bp Total written (filtered): 7,976,083 bp (100.0%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 859 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 92.8% C: 4.0% G: 2.9% T: 0.3% 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 3 852 453.8 0 852 4 4 113.4 0 4 5 1 28.4 0 1 6 2 7.1 0 2 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.