This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TGATCC -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 95.56 s (28 us/read; 2.18 M reads/minute). === Summary === Total reads processed: 3,465,239 Reads with adapters: 432,293 (12.5%) Reads that were too short: 8,885 (0.3%) Reads written (passing filters): 423,408 (12.2%) Total basepairs processed: 1,043,036,939 bp Total written (filtered): 103,779,438 bp (9.9%) === Adapter 1 === Sequence: TGATCC; Type: regular 5'; Length: 6; Trimmed: 432293 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 92 846.0 0 92 7 97 846.0 0 97 8 1146 846.0 0 1146 9 8527 846.0 0 8527 10 103 846.0 0 103 11 100 846.0 0 100 12 121 846.0 0 121 13 17 846.0 0 17 14 21 846.0 0 21 15 25 846.0 0 25 16 19 846.0 0 19 17 41 846.0 0 41 18 22 846.0 0 22 19 31 846.0 0 31 20 37 846.0 0 37 21 61 846.0 0 61 22 165 846.0 0 165 23 50 846.0 0 50 24 95 846.0 0 95 25 94 846.0 0 94 26 79 846.0 0 79 27 153 846.0 0 153 28 60 846.0 0 60 29 158 846.0 0 158 30 343 846.0 0 343 31 106 846.0 0 106 32 111 846.0 0 111 33 204 846.0 0 204 34 278 846.0 0 278 35 676 846.0 0 676 36 623 846.0 0 623 37 1073 846.0 0 1073 38 1288 846.0 0 1288 39 43217 846.0 0 43217 40 15804 846.0 0 15804 41 22772 846.0 0 22772 42 383 846.0 0 383 43 410 846.0 0 410 44 910 846.0 0 910 45 2338 846.0 0 2338 46 2398 846.0 0 2398 47 342 846.0 0 342 48 447 846.0 0 447 49 948 846.0 0 948 50 1718 846.0 0 1718 51 1001 846.0 0 1001 52 764 846.0 0 764 53 935 846.0 0 935 54 1125 846.0 0 1125 55 1211 846.0 0 1211 56 1733 846.0 0 1733 57 2295 846.0 0 2295 58 6582 846.0 0 6582 59 202438 846.0 0 202438 60 30838 846.0 0 30838 61 55450 846.0 0 55450 62 504 846.0 0 504 63 16 846.0 0 16 64 12 846.0 0 12 65 7 846.0 0 7 66 3 846.0 0 3 67 4 846.0 0 4 68 5 846.0 0 5 69 7 846.0 0 7 70 11 846.0 0 11 71 16 846.0 0 16 72 155 846.0 0 155 73 196 846.0 0 196 74 57 846.0 0 57 75 82 846.0 0 82 76 11 846.0 0 11 77 2 846.0 0 2 78 5 846.0 0 5 79 24 846.0 0 24 80 18 846.0 0 18 81 72 846.0 0 72 82 386 846.0 0 386 83 37 846.0 0 37 84 25 846.0 0 25 85 33 846.0 0 33 86 21 846.0 0 21 87 13 846.0 0 13 88 33 846.0 0 33 89 29 846.0 0 29 90 80 846.0 0 80 91 49 846.0 0 49 92 46 846.0 0 46 93 17 846.0 0 17 94 16 846.0 0 16 95 31 846.0 0 31 96 44 846.0 0 44 97 20 846.0 0 20 98 33 846.0 0 33 99 91 846.0 0 91 100 54 846.0 0 54 101 359 846.0 0 359 102 848 846.0 0 848 103 152 846.0 0 152 104 26 846.0 0 26 105 18 846.0 0 18 106 20 846.0 0 20 107 7 846.0 0 7 108 7 846.0 0 7 109 13 846.0 0 13 110 21 846.0 0 21 111 38 846.0 0 38 112 33 846.0 0 33 113 220 846.0 0 220 114 14 846.0 0 14 115 21 846.0 0 21 116 18 846.0 0 18 117 86 846.0 0 86 118 61 846.0 0 61 119 39 846.0 0 39 120 23 846.0 0 23 121 34 846.0 0 34 122 28 846.0 0 28 123 36 846.0 0 36 124 48 846.0 0 48 125 69 846.0 0 69 126 23 846.0 0 23 127 33 846.0 0 33 128 16 846.0 0 16 129 46 846.0 0 46 130 88 846.0 0 88 131 55 846.0 0 55 132 73 846.0 0 73 133 51 846.0 0 51 134 28 846.0 0 28 135 35 846.0 0 35 136 44 846.0 0 44 137 50 846.0 0 50 138 46 846.0 0 46 139 43 846.0 0 43 140 25 846.0 0 25 141 50 846.0 0 50 142 55 846.0 0 55 143 64 846.0 0 64 144 59 846.0 0 59 145 25 846.0 0 25 146 42 846.0 0 42 147 33 846.0 0 33 148 177 846.0 0 177 149 62 846.0 0 62 150 56 846.0 0 56 151 42 846.0 0 42 152 53 846.0 0 53 153 39 846.0 0 39 154 35 846.0 0 35 155 42 846.0 0 42 156 97 846.0 0 97 157 60 846.0 0 60 158 66 846.0 0 66 159 75 846.0 0 75 160 30 846.0 0 30 161 121 846.0 0 121 162 71 846.0 0 71 163 88 846.0 0 88 164 70 846.0 0 70 165 50 846.0 0 50 166 51 846.0 0 51 167 66 846.0 0 66 168 74 846.0 0 74 169 167 846.0 0 167 170 135 846.0 0 135 171 188 846.0 0 188 172 46 846.0 0 46 173 37 846.0 0 37 174 21 846.0 0 21 175 24 846.0 0 24 176 73 846.0 0 73 177 104 846.0 0 104 178 126 846.0 0 126 179 90 846.0 0 90 180 28 846.0 0 28 181 57 846.0 0 57 182 37 846.0 0 37 183 94 846.0 0 94 184 98 846.0 0 98 185 84 846.0 0 84 186 100 846.0 0 100 187 110 846.0 0 110 188 143 846.0 0 143 189 93 846.0 0 93 190 40 846.0 0 40 191 28 846.0 0 28 192 40 846.0 0 40 193 44 846.0 0 44 194 50 846.0 0 50 195 77 846.0 0 77 196 124 846.0 0 124 197 105 846.0 0 105 198 419 846.0 0 419 199 1175 846.0 0 1175 200 346 846.0 0 346 201 117 846.0 0 117 202 72 846.0 0 72 203 92 846.0 0 92 204 99 846.0 0 99 205 223 846.0 0 223 206 70 846.0 0 70 207 66 846.0 0 66 208 53 846.0 0 53 209 59 846.0 0 59 210 59 846.0 0 59 211 40 846.0 0 40 212 82 846.0 0 82 213 90 846.0 0 90 214 89 846.0 0 89 215 58 846.0 0 58 216 52 846.0 0 52 217 65 846.0 0 65 218 53 846.0 0 53 219 58 846.0 0 58 220 80 846.0 0 80 221 81 846.0 0 81 222 101 846.0 0 101 223 193 846.0 0 193 224 198 846.0 0 198 225 348 846.0 0 348 226 188 846.0 0 188 227 469 846.0 0 469 228 1060 846.0 0 1060 229 672 846.0 0 672 230 61 846.0 0 61 231 43 846.0 0 43 232 39 846.0 0 39 233 29 846.0 0 29 234 54 846.0 0 54 235 44 846.0 0 44 236 45 846.0 0 45 237 55 846.0 0 55 238 58 846.0 0 58 239 31 846.0 0 31 240 31 846.0 0 31 241 59 846.0 0 59 242 62 846.0 0 62 243 58 846.0 0 58 244 71 846.0 0 71 245 57 846.0 0 57 246 31 846.0 0 31 247 37 846.0 0 37 248 47 846.0 0 47 249 54 846.0 0 54 250 46 846.0 0 46 251 52 846.0 0 52 252 34 846.0 0 34 253 39 846.0 0 39 254 77 846.0 0 77 255 70 846.0 0 70 256 88 846.0 0 88 257 88 846.0 0 88 258 95 846.0 0 95 259 43 846.0 0 43 260 42 846.0 0 42 261 37 846.0 0 37 262 24 846.0 0 24 263 92 846.0 0 92 264 92 846.0 0 92 265 53 846.0 0 53 266 45 846.0 0 45 267 26 846.0 0 26 268 21 846.0 0 21 269 39 846.0 0 39 270 57 846.0 0 57 271 91 846.0 0 91 272 58 846.0 0 58 273 107 846.0 0 107 274 128 846.0 0 128 275 60 846.0 0 60 276 87 846.0 0 87 277 62 846.0 0 62 278 15 846.0 0 15 279 22 846.0 0 22 280 25 846.0 0 25 281 73 846.0 0 73 282 50 846.0 0 50 283 48 846.0 0 48 284 59 846.0 0 59 285 139 846.0 0 139 286 35 846.0 0 35 287 24 846.0 0 24 288 52 846.0 0 52 289 45 846.0 0 45 290 75 846.0 0 75 291 96 846.0 0 96 292 48 846.0 0 48 293 73 846.0 0 73 294 149 846.0 0 149 295 99 846.0 0 99 296 43 846.0 0 43 297 55 846.0 0 55 298 42 846.0 0 42 299 48 846.0 0 48 300 39 846.0 0 39 301 42 846.0 0 42 Finished in 18.67 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 423,408 Reads with adapters: 3,626 (0.9%) Reads that were too short: 159 (0.0%) Reads written (passing filters): 3,467 (0.8%) Total basepairs processed: 103,779,438 bp Total written (filtered): 688,469 bp (0.7%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 3626 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 3 0.0 3 0 0 1 1 1 19 6 0.0 3 0 6 20 1046 0.0 4 1028 17 0 0 1 21 4 0.0 4 0 3 0 1 22 1 0.0 4 0 0 0 0 1 23 3 0.0 4 0 0 0 3 24 2 0.0 4 2 37 1 0.0 4 0 0 0 0 1 39 1 0.0 4 0 0 0 0 1 40 2 0.0 4 0 0 0 0 2 43 1 0.0 4 0 0 0 1 48 1 0.0 4 0 0 0 0 1 73 6 0.0 4 0 0 0 0 6 74 3 0.0 4 0 0 0 0 3 75 2308 0.0 4 0 0 0 0 2308 77 3 0.0 4 0 0 0 0 3 78 2 0.0 4 0 0 0 0 2 81 1 0.0 4 0 0 0 0 1 83 1 0.0 4 0 0 0 0 1 88 1 0.0 4 0 0 0 0 1 95 1 0.0 4 0 0 0 0 1 99 1 0.0 4 0 0 0 0 1 101 1 0.0 4 0 0 0 0 1 110 1 0.0 4 0 0 0 0 1 125 1 0.0 4 0 0 0 0 1 126 52 0.0 4 0 0 0 0 52 127 1 0.0 4 0 0 0 0 1 131 2 0.0 4 0 0 0 0 2 136 1 0.0 4 0 0 0 0 1 139 11 0.0 4 0 0 0 0 11 144 1 0.0 4 0 0 0 0 1 150 1 0.0 4 0 0 0 0 1 151 1 0.0 4 0 0 0 0 1 155 1 0.0 4 0 0 0 0 1 156 1 0.0 4 0 0 0 0 1 157 1 0.0 4 1 169 1 0.0 4 0 0 0 0 1 170 1 0.0 4 0 0 0 0 1 173 3 0.0 4 0 0 0 0 3 174 1 0.0 4 0 0 0 0 1 175 2 0.0 4 0 0 0 0 2 176 38 0.0 4 0 0 0 1 37 177 6 0.0 4 0 0 0 0 6 178 3 0.0 4 0 0 0 2 1 180 1 0.0 4 0 0 0 0 1 181 3 0.0 4 0 0 0 0 3 182 4 0.0 4 0 0 0 1 3 183 3 0.0 4 0 0 0 0 3 184 2 0.0 4 0 0 0 0 2 186 1 0.0 4 0 0 0 0 1 187 1 0.0 4 0 0 0 0 1 197 1 0.0 4 0 0 0 0 1 201 2 0.0 4 0 0 0 0 2 202 1 0.0 4 0 0 0 0 1 204 1 0.0 4 0 0 0 0 1 206 1 0.0 4 0 0 0 0 1 210 1 0.0 4 0 0 0 0 1 229 2 0.0 4 0 0 0 0 2 230 60 0.0 4 0 0 0 0 60 231 3 0.0 4 0 0 0 0 3 233 1 0.0 4 0 0 0 0 1 237 4 0.0 4 0 0 0 0 4 239 1 0.0 4 0 0 0 0 1 242 1 0.0 4 0 0 0 0 1 244 1 0.0 4 0 0 0 0 1 254 1 0.0 4 0 0 0 0 1 281 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 0.10 s (29 us/read; 2.08 M reads/minute). === Summary === Total reads processed: 3,467 Reads with adapters: 138 (4.0%) Reads written (passing filters): 3,467 (100.0%) Total basepairs processed: 688,469 bp Total written (filtered): 686,782 bp (99.8%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 138 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 10.1% C: 6.5% G: 81.2% T: 2.2% none/other: 0.0% WARNING: The adapter is preceded by "G" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "G" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 3 1 54.2 0 1 4 10 13.5 0 10 10 14 0.0 1 1 13 11 111 0.0 1 0 111 12 1 0.0 1 0 1 271 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.