This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGCTGG -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 91.68 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 3,465,239 Reads with adapters: 304,867 (8.8%) Reads that were too short: 55,769 (1.6%) Reads written (passing filters): 249,098 (7.2%) Total basepairs processed: 1,043,036,939 bp Total written (filtered): 50,548,776 bp (4.8%) === Adapter 1 === Sequence: AGCTGG; Type: regular 5'; Length: 6; Trimmed: 304867 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 337 846.0 0 337 7 4753 846.0 0 4753 8 273 846.0 0 273 9 7242 846.0 0 7242 10 430 846.0 0 430 11 21689 846.0 0 21689 12 92 846.0 0 92 13 41 846.0 0 41 14 59 846.0 0 59 15 47 846.0 0 47 16 42 846.0 0 42 17 28 846.0 0 28 18 44 846.0 0 44 19 34 846.0 0 34 20 48 846.0 0 48 21 42 846.0 0 42 22 64 846.0 0 64 23 33 846.0 0 33 24 43 846.0 0 43 25 53 846.0 0 53 26 56 846.0 0 56 27 34 846.0 0 34 28 46 846.0 0 46 29 52 846.0 0 52 30 48 846.0 0 48 31 72 846.0 0 72 32 59 846.0 0 59 33 45 846.0 0 45 34 77 846.0 0 77 35 184 846.0 0 184 36 68 846.0 0 68 37 57 846.0 0 57 38 55 846.0 0 55 39 56 846.0 0 56 40 49 846.0 0 49 41 46 846.0 0 46 42 53 846.0 0 53 43 66 846.0 0 66 44 1238 846.0 0 1238 45 66 846.0 0 66 46 49 846.0 0 49 47 67 846.0 0 67 48 49 846.0 0 49 49 39 846.0 0 39 50 64 846.0 0 64 51 51 846.0 0 51 52 59 846.0 0 59 53 45 846.0 0 45 54 53 846.0 0 53 55 207 846.0 0 207 56 43 846.0 0 43 57 97 846.0 0 97 58 49 846.0 0 49 59 35 846.0 0 35 60 42 846.0 0 42 61 72 846.0 0 72 62 63 846.0 0 63 63 61 846.0 0 61 64 73 846.0 0 73 65 44 846.0 0 44 66 42 846.0 0 42 67 74 846.0 0 74 68 40 846.0 0 40 69 52 846.0 0 52 70 57 846.0 0 57 71 98 846.0 0 98 72 40 846.0 0 40 73 44 846.0 0 44 74 35 846.0 0 35 75 52 846.0 0 52 76 40 846.0 0 40 77 36 846.0 0 36 78 44 846.0 0 44 79 318 846.0 0 318 80 50 846.0 0 50 81 140 846.0 0 140 82 42 846.0 0 42 83 202 846.0 0 202 84 73 846.0 0 73 85 139 846.0 0 139 86 52 846.0 0 52 87 75 846.0 0 75 88 62 846.0 0 62 89 290 846.0 0 290 90 107 846.0 0 107 91 96 846.0 0 96 92 52 846.0 0 52 93 189 846.0 0 189 94 90 846.0 0 90 95 92 846.0 0 92 96 159 846.0 0 159 97 328 846.0 0 328 98 697 846.0 0 697 99 1568 846.0 0 1568 100 1140 846.0 0 1140 101 202 846.0 0 202 102 206 846.0 0 206 103 345 846.0 0 345 104 1597 846.0 0 1597 105 778 846.0 0 778 106 405 846.0 0 405 107 519 846.0 0 519 108 401 846.0 0 401 109 639 846.0 0 639 110 980 846.0 0 980 111 1214 846.0 0 1214 112 4553 846.0 0 4553 113 173241 846.0 0 173241 114 3131 846.0 0 3131 115 7075 846.0 0 7075 116 86 846.0 0 86 117 36 846.0 0 36 118 52 846.0 0 52 119 45 846.0 0 45 120 47 846.0 0 47 121 39 846.0 0 39 122 49 846.0 0 49 123 39 846.0 0 39 124 44 846.0 0 44 125 51 846.0 0 51 126 57 846.0 0 57 127 61 846.0 0 61 128 39 846.0 0 39 129 61 846.0 0 61 130 310 846.0 0 310 131 931 846.0 0 931 132 73 846.0 0 73 133 46 846.0 0 46 134 54 846.0 0 54 135 49 846.0 0 49 136 51 846.0 0 51 137 49 846.0 0 49 138 50 846.0 0 50 139 50 846.0 0 50 140 57 846.0 0 57 141 69 846.0 0 69 142 54 846.0 0 54 143 160 846.0 0 160 144 156 846.0 0 156 145 47 846.0 0 47 146 44 846.0 0 44 147 50 846.0 0 50 148 124 846.0 0 124 149 68 846.0 0 68 150 44 846.0 0 44 151 40 846.0 0 40 152 32 846.0 0 32 153 55 846.0 0 55 154 91 846.0 0 91 155 487 846.0 0 487 156 797 846.0 0 797 157 168 846.0 0 168 158 447 846.0 0 447 159 37 846.0 0 37 160 35 846.0 0 35 161 35 846.0 0 35 162 54 846.0 0 54 163 62 846.0 0 62 164 60 846.0 0 60 165 51 846.0 0 51 166 40 846.0 0 40 167 111 846.0 0 111 168 278 846.0 0 278 169 203 846.0 0 203 170 33 846.0 0 33 171 51 846.0 0 51 172 43 846.0 0 43 173 38 846.0 0 38 174 53 846.0 0 53 175 54 846.0 0 54 176 37 846.0 0 37 177 45 846.0 0 45 178 44 846.0 0 44 179 31 846.0 0 31 180 59 846.0 0 59 181 37 846.0 0 37 182 44 846.0 0 44 183 46 846.0 0 46 184 33 846.0 0 33 185 51 846.0 0 51 186 31 846.0 0 31 187 44 846.0 0 44 188 55 846.0 0 55 189 83 846.0 0 83 190 56 846.0 0 56 191 56 846.0 0 56 192 50 846.0 0 50 193 44 846.0 0 44 194 37 846.0 0 37 195 46 846.0 0 46 196 51 846.0 0 51 197 61 846.0 0 61 198 47 846.0 0 47 199 57 846.0 0 57 200 134 846.0 0 134 201 238 846.0 0 238 202 375 846.0 0 375 203 108 846.0 0 108 204 67 846.0 0 67 205 53 846.0 0 53 206 56 846.0 0 56 207 36 846.0 0 36 208 41 846.0 0 41 209 64 846.0 0 64 210 68 846.0 0 68 211 47 846.0 0 47 212 71 846.0 0 71 213 62 846.0 0 62 214 71 846.0 0 71 215 42 846.0 0 42 216 77 846.0 0 77 217 83 846.0 0 83 218 126 846.0 0 126 219 50 846.0 0 50 220 34 846.0 0 34 221 59 846.0 0 59 222 42 846.0 0 42 223 47 846.0 0 47 224 37 846.0 0 37 225 63 846.0 0 63 226 54 846.0 0 54 227 51 846.0 0 51 228 156 846.0 0 156 229 55 846.0 0 55 230 130 846.0 0 130 231 59 846.0 0 59 232 62 846.0 0 62 233 226 846.0 0 226 234 53 846.0 0 53 235 43 846.0 0 43 236 81 846.0 0 81 237 69 846.0 0 69 238 26 846.0 0 26 239 52 846.0 0 52 240 40 846.0 0 40 241 43 846.0 0 43 242 41 846.0 0 41 243 76 846.0 0 76 244 41 846.0 0 41 245 48 846.0 0 48 246 61 846.0 0 61 247 34 846.0 0 34 248 48 846.0 0 48 249 37 846.0 0 37 250 22 846.0 0 22 251 44 846.0 0 44 252 125 846.0 0 125 253 66 846.0 0 66 254 47 846.0 0 47 255 112 846.0 0 112 256 58 846.0 0 58 257 66 846.0 0 66 258 49 846.0 0 49 259 56 846.0 0 56 260 57 846.0 0 57 261 54 846.0 0 54 262 58 846.0 0 58 263 71 846.0 0 71 264 57 846.0 0 57 265 42 846.0 0 42 266 44 846.0 0 44 267 41 846.0 0 41 268 53 846.0 0 53 269 52 846.0 0 52 270 89 846.0 0 89 271 75 846.0 0 75 272 61 846.0 0 61 273 37 846.0 0 37 274 68 846.0 0 68 275 29 846.0 0 29 276 59 846.0 0 59 277 37 846.0 0 37 278 46 846.0 0 46 279 56 846.0 0 56 280 74 846.0 0 74 281 105 846.0 0 105 282 79 846.0 0 79 283 91 846.0 0 91 284 251 846.0 0 251 285 346 846.0 0 346 286 85 846.0 0 85 287 122 846.0 0 122 288 178 846.0 0 178 289 99 846.0 0 99 290 104 846.0 0 104 291 212 846.0 0 212 292 272 846.0 0 272 293 190 846.0 0 190 294 206 846.0 0 206 295 302 846.0 0 302 296 1080 846.0 0 1080 297 14512 846.0 0 14512 298 9223 846.0 0 9223 299 7347 846.0 0 7347 300 15702 846.0 0 15702 301 93 846.0 0 93 Finished in 10.05 s (40 us/read; 1.49 M reads/minute). === Summary === Total reads processed: 249,098 Reads with adapters: 7,285 (2.9%) Reads that were too short: 15 (0.0%) Reads written (passing filters): 7,270 (2.9%) Total basepairs processed: 50,548,776 bp Total written (filtered): 1,976,123 bp (3.9%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 7285 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 0 4 18 3 0.0 3 0 0 3 19 85 0.0 3 0 82 1 1 1 20 7121 0.0 4 7038 72 1 4 6 21 18 0.0 4 6 12 22 3 0.0 4 0 0 2 0 1 23 3 0.0 4 0 0 0 3 24 3 0.0 4 0 0 0 2 1 25 1 0.0 4 0 1 26 1 0.0 4 1 29 1 0.0 4 1 31 1 0.0 4 0 1 35 6 0.0 4 0 0 0 1 5 37 1 0.0 4 0 0 0 1 45 1 0.0 4 0 1 46 2 0.0 4 0 2 47 5 0.0 4 0 0 0 0 5 48 6 0.0 4 0 0 0 0 6 66 1 0.0 4 0 0 0 0 1 77 1 0.0 4 0 0 0 0 1 93 1 0.0 4 0 0 0 0 1 94 1 0.0 4 0 0 0 0 1 127 3 0.0 4 0 0 0 0 3 139 1 0.0 4 0 0 0 0 1 151 6 0.0 4 0 0 0 0 6 152 1 0.0 4 0 0 0 0 1 176 1 0.0 4 0 0 0 0 1 177 2 0.0 4 1 0 0 0 1 202 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 0.24 s (33 us/read; 1.82 M reads/minute). === Summary === Total reads processed: 7,270 Reads with adapters: 5,268 (72.5%) Reads written (passing filters): 7,270 (100.0%) Total basepairs processed: 1,976,123 bp Total written (filtered): 580,449 bp (29.4%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 5268 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 12.5% C: 0.3% G: 87.0% T: 0.2% 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 2 113.6 0 2 4 3 28.4 0 3 9 2 0.0 0 1 1 10 34 0.0 1 1 33 11 4 0.0 1 0 4 228 5 0.0 1 3 2 229 1 0.0 1 1 230 8 0.0 1 7 1 238 1 0.0 1 1 245 1 0.0 1 1 255 1 0.0 1 1 256 1 0.0 1 1 257 625 0.0 1 579 46 258 15 0.0 1 15 259 6 0.0 1 6 260 2 0.0 1 1 1 261 4 0.0 1 4 262 6 0.0 1 5 1 263 2 0.0 1 2 266 6 0.0 1 6 267 703 0.0 1 680 23 268 39 0.0 1 39 269 3658 0.0 1 3512 146 270 96 0.0 1 94 2 271 27 0.0 1 27 272 16 0.0 1 16 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.