This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AAGTGT -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 171.54 s (47 us/read; 1.27 M reads/minute). === Summary === Total reads processed: 3,634,272 Reads with adapters: 233,361 (6.4%) Reads that were too short: 19,021 (0.5%) Reads written (passing filters): 214,340 (5.9%) Total basepairs processed: 1,093,915,872 bp Total written (filtered): 59,340,364 bp (5.4%) === Adapter 1 === Sequence: AAGTGT; Type: regular 5'; Length: 6; Trimmed: 233361 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1861 887.3 0 1861 7 102259 887.3 0 102259 8 82562 887.3 0 82562 9 98 887.3 0 98 10 59 887.3 0 59 11 53 887.3 0 53 12 50 887.3 0 50 13 55 887.3 0 55 14 29 887.3 0 29 15 38 887.3 0 38 16 44 887.3 0 44 17 30 887.3 0 30 18 50 887.3 0 50 19 35 887.3 0 35 20 50 887.3 0 50 21 56 887.3 0 56 22 83 887.3 0 83 23 49 887.3 0 49 24 31 887.3 0 31 25 27 887.3 0 27 26 39 887.3 0 39 27 76 887.3 0 76 28 58 887.3 0 58 29 244 887.3 0 244 30 49 887.3 0 49 31 323 887.3 0 323 32 47 887.3 0 47 33 37 887.3 0 37 34 51 887.3 0 51 35 37 887.3 0 37 36 41 887.3 0 41 37 53 887.3 0 53 38 45 887.3 0 45 39 45 887.3 0 45 40 49 887.3 0 49 41 32 887.3 0 32 42 35 887.3 0 35 43 35 887.3 0 35 44 36 887.3 0 36 45 59 887.3 0 59 46 51 887.3 0 51 47 46 887.3 0 46 48 55 887.3 0 55 49 32 887.3 0 32 50 34 887.3 0 34 51 32 887.3 0 32 52 62 887.3 0 62 53 39 887.3 0 39 54 171 887.3 0 171 55 371 887.3 0 371 56 189 887.3 0 189 57 35 887.3 0 35 58 49 887.3 0 49 59 43 887.3 0 43 60 62 887.3 0 62 61 321 887.3 0 321 62 471 887.3 0 471 63 476 887.3 0 476 64 40 887.3 0 40 65 44 887.3 0 44 66 41 887.3 0 41 67 211 887.3 0 211 68 178 887.3 0 178 69 281 887.3 0 281 70 43 887.3 0 43 71 81 887.3 0 81 72 71 887.3 0 71 73 427 887.3 0 427 74 127 887.3 0 127 75 94 887.3 0 94 76 62 887.3 0 62 77 38 887.3 0 38 78 70 887.3 0 70 79 88 887.3 0 88 80 79 887.3 0 79 81 69 887.3 0 69 82 62 887.3 0 62 83 102 887.3 0 102 84 80 887.3 0 80 85 143 887.3 0 143 86 188 887.3 0 188 87 127 887.3 0 127 88 121 887.3 0 121 89 59 887.3 0 59 90 56 887.3 0 56 91 42 887.3 0 42 92 53 887.3 0 53 93 37 887.3 0 37 94 94 887.3 0 94 95 49 887.3 0 49 96 43 887.3 0 43 97 73 887.3 0 73 98 89 887.3 0 89 99 54 887.3 0 54 100 54 887.3 0 54 101 48 887.3 0 48 102 44 887.3 0 44 103 40 887.3 0 40 104 35 887.3 0 35 105 34 887.3 0 34 106 47 887.3 0 47 107 31 887.3 0 31 108 40 887.3 0 40 109 41 887.3 0 41 110 31 887.3 0 31 111 48 887.3 0 48 112 82 887.3 0 82 113 69 887.3 0 69 114 57 887.3 0 57 115 65 887.3 0 65 116 47 887.3 0 47 117 44 887.3 0 44 118 50 887.3 0 50 119 52 887.3 0 52 120 61 887.3 0 61 121 59 887.3 0 59 122 65 887.3 0 65 123 176 887.3 0 176 124 164 887.3 0 164 125 166 887.3 0 166 126 183 887.3 0 183 127 251 887.3 0 251 128 392 887.3 0 392 129 844 887.3 0 844 130 414 887.3 0 414 131 319 887.3 0 319 132 154 887.3 0 154 133 98 887.3 0 98 134 176 887.3 0 176 135 181 887.3 0 181 136 149 887.3 0 149 137 45 887.3 0 45 138 91 887.3 0 91 139 75 887.3 0 75 140 63 887.3 0 63 141 71 887.3 0 71 142 69 887.3 0 69 143 66 887.3 0 66 144 130 887.3 0 130 145 541 887.3 0 541 146 87 887.3 0 87 147 50 887.3 0 50 148 86 887.3 0 86 149 96 887.3 0 96 150 79 887.3 0 79 151 90 887.3 0 90 152 91 887.3 0 91 153 57 887.3 0 57 154 73 887.3 0 73 155 72 887.3 0 72 156 147 887.3 0 147 157 133 887.3 0 133 158 95 887.3 0 95 159 68 887.3 0 68 160 69 887.3 0 69 161 59 887.3 0 59 162 53 887.3 0 53 163 59 887.3 0 59 164 56 887.3 0 56 165 75 887.3 0 75 166 212 887.3 0 212 167 119 887.3 0 119 168 181 887.3 0 181 169 51 887.3 0 51 170 55 887.3 0 55 171 54 887.3 0 54 172 79 887.3 0 79 173 66 887.3 0 66 174 108 887.3 0 108 175 87 887.3 0 87 176 96 887.3 0 96 177 59 887.3 0 59 178 70 887.3 0 70 179 68 887.3 0 68 180 54 887.3 0 54 181 58 887.3 0 58 182 79 887.3 0 79 183 86 887.3 0 86 184 100 887.3 0 100 185 99 887.3 0 99 186 86 887.3 0 86 187 109 887.3 0 109 188 74 887.3 0 74 189 72 887.3 0 72 190 88 887.3 0 88 191 110 887.3 0 110 192 130 887.3 0 130 193 120 887.3 0 120 194 173 887.3 0 173 195 304 887.3 0 304 196 1265 887.3 0 1265 197 2053 887.3 0 2053 198 2580 887.3 0 2580 199 2601 887.3 0 2601 200 180 887.3 0 180 201 92 887.3 0 92 202 87 887.3 0 87 203 68 887.3 0 68 204 76 887.3 0 76 205 64 887.3 0 64 206 70 887.3 0 70 207 111 887.3 0 111 208 113 887.3 0 113 209 79 887.3 0 79 210 127 887.3 0 127 211 314 887.3 0 314 212 175 887.3 0 175 213 156 887.3 0 156 214 100 887.3 0 100 215 114 887.3 0 114 216 74 887.3 0 74 217 75 887.3 0 75 218 122 887.3 0 122 219 241 887.3 0 241 220 331 887.3 0 331 221 309 887.3 0 309 222 247 887.3 0 247 223 168 887.3 0 168 224 304 887.3 0 304 225 116 887.3 0 116 226 107 887.3 0 107 227 135 887.3 0 135 228 63 887.3 0 63 229 63 887.3 0 63 230 52 887.3 0 52 231 78 887.3 0 78 232 97 887.3 0 97 233 100 887.3 0 100 234 66 887.3 0 66 235 89 887.3 0 89 236 86 887.3 0 86 237 97 887.3 0 97 238 240 887.3 0 240 239 225 887.3 0 225 240 356 887.3 0 356 241 326 887.3 0 326 242 262 887.3 0 262 243 143 887.3 0 143 244 164 887.3 0 164 245 998 887.3 0 998 246 746 887.3 0 746 247 856 887.3 0 856 248 195 887.3 0 195 249 200 887.3 0 200 250 169 887.3 0 169 251 108 887.3 0 108 252 67 887.3 0 67 253 70 887.3 0 70 254 199 887.3 0 199 255 190 887.3 0 190 256 131 887.3 0 131 257 74 887.3 0 74 258 87 887.3 0 87 259 109 887.3 0 109 260 147 887.3 0 147 261 138 887.3 0 138 262 428 887.3 0 428 263 1430 887.3 0 1430 264 392 887.3 0 392 265 88 887.3 0 88 266 113 887.3 0 113 267 435 887.3 0 435 268 737 887.3 0 737 269 637 887.3 0 637 270 263 887.3 0 263 271 62 887.3 0 62 272 137 887.3 0 137 273 286 887.3 0 286 274 299 887.3 0 299 275 257 887.3 0 257 276 178 887.3 0 178 277 95 887.3 0 95 278 57 887.3 0 57 279 81 887.3 0 81 280 88 887.3 0 88 281 161 887.3 0 161 282 160 887.3 0 160 283 126 887.3 0 126 284 57 887.3 0 57 285 66 887.3 0 66 286 66 887.3 0 66 287 86 887.3 0 86 288 149 887.3 0 149 289 158 887.3 0 158 290 112 887.3 0 112 291 75 887.3 0 75 292 83 887.3 0 83 293 56 887.3 0 56 294 100 887.3 0 100 295 91 887.3 0 91 296 103 887.3 0 103 297 91 887.3 0 91 298 63 887.3 0 63 299 107 887.3 0 107 300 111 887.3 0 111 301 63 887.3 0 63 Finished in 16.75 s (78 us/read; 0.77 M reads/minute). === Summary === Total reads processed: 214,340 Reads with adapters: 88,145 (41.1%) Reads that were too short: 90 (0.0%) Reads written (passing filters): 88,055 (41.1%) Total basepairs processed: 59,340,364 bp Total written (filtered): 23,905,208 bp (40.3%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 88145 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 4 0.0 3 0 0 0 3 1 18 39 0.0 3 0 0 28 9 2 19 989 0.0 3 0 839 67 59 24 20 85175 0.0 4 81200 3270 539 133 33 21 261 0.0 4 35 204 15 2 5 22 31 0.0 4 8 1 19 0 3 23 250 0.0 4 8 1 0 184 57 24 4 0.0 4 1 0 0 0 3 25 1 0.0 4 1 26 4 0.0 4 1 3 27 1 0.0 4 0 0 1 31 1 0.0 4 0 1 32 2 0.0 4 0 0 0 0 2 37 1 0.0 4 0 0 0 0 1 39 2 0.0 4 1 0 0 0 1 42 1 0.0 4 0 0 1 48 1 0.0 4 0 0 0 0 1 59 1 0.0 4 0 0 0 0 1 67 1 0.0 4 0 0 0 0 1 70 1 0.0 4 0 0 0 0 1 74 1 0.0 4 0 0 0 0 1 83 1 0.0 4 0 0 0 0 1 89 1 0.0 4 0 0 0 0 1 92 2 0.0 4 0 0 0 0 2 98 1 0.0 4 0 0 0 0 1 107 1 0.0 4 0 0 0 0 1 116 1 0.0 4 0 0 0 0 1 118 1 0.0 4 0 0 0 0 1 123 1 0.0 4 1 125 7 0.0 4 0 0 0 0 7 126 12 0.0 4 0 0 0 0 12 127 1238 0.0 4 0 0 0 1 1237 128 8 0.0 4 0 0 0 0 8 130 2 0.0 4 0 0 0 0 2 136 1 0.0 4 0 0 0 0 1 140 2 0.0 4 0 0 0 0 2 143 1 0.0 4 0 0 0 0 1 152 3 0.0 4 0 0 0 0 3 153 13 0.0 4 0 0 0 1 12 154 2 0.0 4 0 0 0 0 2 202 1 0.0 4 0 0 0 0 1 203 1 0.0 4 0 0 0 0 1 205 1 0.0 4 0 0 0 0 1 207 1 0.0 4 0 0 0 0 1 208 2 0.0 4 0 0 0 0 2 211 1 0.0 4 0 0 0 0 1 213 1 0.0 4 0 0 0 0 1 216 1 0.0 4 0 0 0 0 1 225 1 0.0 4 0 0 0 0 1 227 1 0.0 4 0 0 0 0 1 228 16 0.0 4 0 0 0 0 16 229 6 0.0 4 0 0 0 2 4 232 2 0.0 4 0 0 0 0 2 233 2 0.0 4 0 0 0 0 2 234 3 0.0 4 0 0 0 0 3 235 2 0.0 4 0 0 0 0 2 236 1 0.0 4 0 0 0 0 1 237 1 0.0 4 0 0 0 0 1 257 1 0.0 4 0 0 0 0 1 258 1 0.0 4 0 0 0 0 1 262 1 0.0 4 0 0 0 0 1 263 2 0.0 4 0 0 0 1 1 279 1 0.0 4 0 0 0 0 1 282 4 0.0 4 0 0 0 0 4 285 1 0.0 4 0 0 0 0 1 288 13 0.0 4 0 0 0 0 13 289 3 0.0 4 0 0 0 0 3 292 1 0.0 4 0 0 0 0 1 293 2 0.0 4 0 0 0 0 2 294 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 5.19 s (59 us/read; 1.02 M reads/minute). === Summary === Total reads processed: 88,055 Reads with adapters: 14,075 (16.0%) Reads written (passing filters): 88,055 (100.0%) Total basepairs processed: 23,905,208 bp Total written (filtered): 23,745,637 bp (99.3%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 14075 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 2.2% C: 6.2% G: 89.5% 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 3 197 1375.9 0 197 4 46 344.0 0 46 5 3 86.0 0 3 6 13 21.5 0 13 7 2 5.4 0 2 8 4 1.3 0 4 9 107 0.3 0 7 100 10 1408 0.1 1 83 1325 11 12124 0.0 1 269 11855 12 109 0.0 1 2 107 13 5 0.0 1 0 5 14 11 0.0 1 0 11 15 5 0.0 1 0 5 151 6 0.0 1 3 3 209 9 0.0 1 9 224 23 0.0 1 23 225 1 0.0 1 1 226 1 0.0 1 1 258 1 0.0 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.