This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TGCGTG -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 172.34 s (47 us/read; 1.27 M reads/minute). === Summary === Total reads processed: 3,634,272 Reads with adapters: 162,124 (4.5%) Reads that were too short: 45,585 (1.3%) Reads written (passing filters): 116,539 (3.2%) Total basepairs processed: 1,093,915,872 bp Total written (filtered): 30,978,195 bp (2.8%) === Adapter 1 === Sequence: TGCGTG; Type: regular 5'; Length: 6; Trimmed: 162124 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1971 887.3 0 1971 7 37199 887.3 0 37199 8 45996 887.3 0 45996 9 99 887.3 0 99 10 206 887.3 0 206 11 54 887.3 0 54 12 49 887.3 0 49 13 48 887.3 0 48 14 57 887.3 0 57 15 57 887.3 0 57 16 52 887.3 0 52 17 49 887.3 0 49 18 59 887.3 0 59 19 63 887.3 0 63 20 54 887.3 0 54 21 57 887.3 0 57 22 35 887.3 0 35 23 62 887.3 0 62 24 47 887.3 0 47 25 60 887.3 0 60 26 64 887.3 0 64 27 59 887.3 0 59 28 61 887.3 0 61 29 80 887.3 0 80 30 72 887.3 0 72 31 43 887.3 0 43 32 60 887.3 0 60 33 84 887.3 0 84 34 51 887.3 0 51 35 45 887.3 0 45 36 61 887.3 0 61 37 52 887.3 0 52 38 59 887.3 0 59 39 72 887.3 0 72 40 64 887.3 0 64 41 51 887.3 0 51 42 89 887.3 0 89 43 89 887.3 0 89 44 66 887.3 0 66 45 44 887.3 0 44 46 123 887.3 0 123 47 84 887.3 0 84 48 57 887.3 0 57 49 103 887.3 0 103 50 71 887.3 0 71 51 55 887.3 0 55 52 82 887.3 0 82 53 99 887.3 0 99 54 74 887.3 0 74 55 77 887.3 0 77 56 77 887.3 0 77 57 86 887.3 0 86 58 95 887.3 0 95 59 57 887.3 0 57 60 97 887.3 0 97 61 84 887.3 0 84 62 186 887.3 0 186 63 86 887.3 0 86 64 1964 887.3 0 1964 65 85 887.3 0 85 66 68 887.3 0 68 67 74 887.3 0 74 68 81 887.3 0 81 69 57 887.3 0 57 70 97 887.3 0 97 71 85 887.3 0 85 72 111 887.3 0 111 73 728 887.3 0 728 74 734 887.3 0 734 75 513 887.3 0 513 76 124 887.3 0 124 77 1285 887.3 0 1285 78 1463 887.3 0 1463 79 558 887.3 0 558 80 47 887.3 0 47 81 73 887.3 0 73 82 66 887.3 0 66 83 46 887.3 0 46 84 44 887.3 0 44 85 77 887.3 0 77 86 59 887.3 0 59 87 56 887.3 0 56 88 61 887.3 0 61 89 74 887.3 0 74 90 63 887.3 0 63 91 76 887.3 0 76 92 60 887.3 0 60 93 65 887.3 0 65 94 58 887.3 0 58 95 80 887.3 0 80 96 56 887.3 0 56 97 94 887.3 0 94 98 72 887.3 0 72 99 76 887.3 0 76 100 75 887.3 0 75 101 86 887.3 0 86 102 56 887.3 0 56 103 71 887.3 0 71 104 89 887.3 0 89 105 89 887.3 0 89 106 266 887.3 0 266 107 430 887.3 0 430 108 544 887.3 0 544 109 77 887.3 0 77 110 67 887.3 0 67 111 65 887.3 0 65 112 97 887.3 0 97 113 113 887.3 0 113 114 73 887.3 0 73 115 142 887.3 0 142 116 92 887.3 0 92 117 88 887.3 0 88 118 87 887.3 0 87 119 81 887.3 0 81 120 105 887.3 0 105 121 81 887.3 0 81 122 87 887.3 0 87 123 218 887.3 0 218 124 96 887.3 0 96 125 119 887.3 0 119 126 76 887.3 0 76 127 170 887.3 0 170 128 1110 887.3 0 1110 129 708 887.3 0 708 130 1509 887.3 0 1509 131 89 887.3 0 89 132 82 887.3 0 82 133 152 887.3 0 152 134 472 887.3 0 472 135 254 887.3 0 254 136 459 887.3 0 459 137 251 887.3 0 251 138 123 887.3 0 123 139 113 887.3 0 113 140 106 887.3 0 106 141 71 887.3 0 71 142 117 887.3 0 117 143 77 887.3 0 77 144 87 887.3 0 87 145 198 887.3 0 198 146 983 887.3 0 983 147 1102 887.3 0 1102 148 638 887.3 0 638 149 131 887.3 0 131 150 71 887.3 0 71 151 56 887.3 0 56 152 56 887.3 0 56 153 71 887.3 0 71 154 94 887.3 0 94 155 236 887.3 0 236 156 279 887.3 0 279 157 462 887.3 0 462 158 90 887.3 0 90 159 89 887.3 0 89 160 85 887.3 0 85 161 76 887.3 0 76 162 73 887.3 0 73 163 60 887.3 0 60 164 149 887.3 0 149 165 132 887.3 0 132 166 158 887.3 0 158 167 76 887.3 0 76 168 56 887.3 0 56 169 68 887.3 0 68 170 64 887.3 0 64 171 66 887.3 0 66 172 43 887.3 0 43 173 48 887.3 0 48 174 52 887.3 0 52 175 54 887.3 0 54 176 35 887.3 0 35 177 56 887.3 0 56 178 40 887.3 0 40 179 61 887.3 0 61 180 73 887.3 0 73 181 52 887.3 0 52 182 55 887.3 0 55 183 61 887.3 0 61 184 165 887.3 0 165 185 175 887.3 0 175 186 137 887.3 0 137 187 95 887.3 0 95 188 65 887.3 0 65 189 44 887.3 0 44 190 43 887.3 0 43 191 57 887.3 0 57 192 80 887.3 0 80 193 63 887.3 0 63 194 69 887.3 0 69 195 483 887.3 0 483 196 443 887.3 0 443 197 195 887.3 0 195 198 73 887.3 0 73 199 78 887.3 0 78 200 70 887.3 0 70 201 72 887.3 0 72 202 53 887.3 0 53 203 80 887.3 0 80 204 61 887.3 0 61 205 74 887.3 0 74 206 80 887.3 0 80 207 50 887.3 0 50 208 56 887.3 0 56 209 85 887.3 0 85 210 79 887.3 0 79 211 45 887.3 0 45 212 70 887.3 0 70 213 58 887.3 0 58 214 60 887.3 0 60 215 224 887.3 0 224 216 207 887.3 0 207 217 134 887.3 0 134 218 101 887.3 0 101 219 111 887.3 0 111 220 70 887.3 0 70 221 57 887.3 0 57 222 77 887.3 0 77 223 205 887.3 0 205 224 79 887.3 0 79 225 83 887.3 0 83 226 57 887.3 0 57 227 72 887.3 0 72 228 69 887.3 0 69 229 88 887.3 0 88 230 111 887.3 0 111 231 156 887.3 0 156 232 146 887.3 0 146 233 249 887.3 0 249 234 332 887.3 0 332 235 415 887.3 0 415 236 5568 887.3 0 5568 237 13968 887.3 0 13968 238 14328 887.3 0 14328 239 160 887.3 0 160 240 73 887.3 0 73 241 68 887.3 0 68 242 80 887.3 0 80 243 74 887.3 0 74 244 51 887.3 0 51 245 104 887.3 0 104 246 195 887.3 0 195 247 248 887.3 0 248 248 297 887.3 0 297 249 168 887.3 0 168 250 86 887.3 0 86 251 156 887.3 0 156 252 143 887.3 0 143 253 184 887.3 0 184 254 90 887.3 0 90 255 95 887.3 0 95 256 74 887.3 0 74 257 45 887.3 0 45 258 61 887.3 0 61 259 55 887.3 0 55 260 57 887.3 0 57 261 48 887.3 0 48 262 58 887.3 0 58 263 72 887.3 0 72 264 79 887.3 0 79 265 85 887.3 0 85 266 109 887.3 0 109 267 63 887.3 0 63 268 59 887.3 0 59 269 57 887.3 0 57 270 53 887.3 0 53 271 57 887.3 0 57 272 81 887.3 0 81 273 79 887.3 0 79 274 90 887.3 0 90 275 43 887.3 0 43 276 51 887.3 0 51 277 98 887.3 0 98 278 88 887.3 0 88 279 67 887.3 0 67 280 147 887.3 0 147 281 200 887.3 0 200 282 274 887.3 0 274 283 154 887.3 0 154 284 261 887.3 0 261 285 234 887.3 0 234 286 129 887.3 0 129 287 83 887.3 0 83 288 86 887.3 0 86 289 105 887.3 0 105 290 61 887.3 0 61 291 76 887.3 0 76 292 71 887.3 0 71 293 125 887.3 0 125 294 139 887.3 0 139 295 224 887.3 0 224 296 310 887.3 0 310 297 335 887.3 0 335 298 387 887.3 0 387 299 163 887.3 0 163 300 151 887.3 0 151 301 211 887.3 0 211 Finished in 8.99 s (77 us/read; 0.78 M reads/minute). === Summary === Total reads processed: 116,539 Reads with adapters: 47,553 (40.8%) Reads that were too short: 20 (0.0%) Reads written (passing filters): 47,533 (40.8%) Total basepairs processed: 30,978,195 bp Total written (filtered): 12,949,397 bp (41.8%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 47553 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 1 0.0 3 0 0 0 1 18 15 0.0 3 0 0 15 19 580 0.0 3 0 568 9 2 1 20 46423 0.0 4 45633 754 35 1 21 115 0.0 4 27 86 1 1 22 101 0.0 4 87 3 10 1 23 24 0.0 4 0 0 0 21 3 24 2 0.0 4 0 1 0 0 1 57 89 0.0 4 0 0 0 0 89 60 1 0.0 4 0 0 0 0 1 61 36 0.0 4 0 0 0 0 36 69 1 0.0 4 0 0 0 0 1 76 2 0.0 4 0 0 0 0 2 83 1 0.0 4 0 0 0 0 1 91 1 0.0 4 0 0 0 1 92 1 0.0 4 0 0 0 0 1 100 1 0.0 4 0 0 0 0 1 102 1 0.0 4 0 0 0 0 1 107 3 0.0 4 0 0 0 0 3 108 4 0.0 4 0 0 0 0 4 111 1 0.0 4 0 0 0 0 1 126 2 0.0 4 0 0 0 0 2 127 137 0.0 4 0 0 0 0 137 132 1 0.0 4 0 0 0 0 1 144 1 0.0 4 0 0 0 0 1 169 1 0.0 4 0 0 0 0 1 170 1 0.0 4 0 0 0 0 1 172 1 0.0 4 0 0 0 0 1 201 1 0.0 4 0 0 0 0 1 228 3 0.0 4 0 0 0 0 3 241 1 0.0 4 0 0 0 0 1 282 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 2.83 s (60 us/read; 1.01 M reads/minute). === Summary === Total reads processed: 47,533 Reads with adapters: 3,632 (7.6%) Reads written (passing filters): 47,533 (100.0%) Total basepairs processed: 12,949,397 bp Total written (filtered): 12,907,383 bp (99.7%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 3632 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.2% C: 2.7% G: 94.4% T: 1.8% 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 32 742.7 0 32 4 11 185.7 0 11 5 3 46.4 0 3 6 1 11.6 0 1 7 1 2.9 0 1 8 1 0.7 0 1 9 52 0.2 0 0 52 10 402 0.0 1 17 385 11 3098 0.0 1 21 3077 12 6 0.0 1 0 6 13 2 0.0 1 0 2 14 2 0.0 1 0 2 59 9 0.0 1 8 1 151 1 0.0 1 0 1 224 11 0.0 1 11 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.