This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CTCTGC -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 69.75 s (26 us/read; 2.33 M reads/minute). === Summary === Total reads processed: 2,708,680 Reads with adapters: 230,649 (8.5%) Reads that were too short: 9,147 (0.3%) Reads written (passing filters): 221,502 (8.2%) Total basepairs processed: 815,312,680 bp Total written (filtered): 40,648,357 bp (5.0%) === Adapter 1 === Sequence: CTCTGC; Type: regular 5'; Length: 6; Trimmed: 230649 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 113 661.3 0 113 7 108 661.3 0 108 8 148 661.3 0 148 9 5703 661.3 0 5703 10 43 661.3 0 43 11 31 661.3 0 31 12 34 661.3 0 34 13 41 661.3 0 41 14 74 661.3 0 74 15 40 661.3 0 40 16 28 661.3 0 28 17 30 661.3 0 30 18 22 661.3 0 22 19 28 661.3 0 28 20 32 661.3 0 32 21 51 661.3 0 51 22 36 661.3 0 36 23 74 661.3 0 74 24 80 661.3 0 80 25 58 661.3 0 58 26 31 661.3 0 31 27 27 661.3 0 27 28 45 661.3 0 45 29 37 661.3 0 37 30 34 661.3 0 34 31 54 661.3 0 54 32 41 661.3 0 41 33 52 661.3 0 52 34 118 661.3 0 118 35 79 661.3 0 79 36 46 661.3 0 46 37 53 661.3 0 53 38 50 661.3 0 50 39 47 661.3 0 47 40 35 661.3 0 35 41 64 661.3 0 64 42 45 661.3 0 45 43 60 661.3 0 60 44 40 661.3 0 40 45 42 661.3 0 42 46 41 661.3 0 41 47 41 661.3 0 41 48 43 661.3 0 43 49 30 661.3 0 30 50 31 661.3 0 31 51 53 661.3 0 53 52 41 661.3 0 41 53 33 661.3 0 33 54 41 661.3 0 41 55 52 661.3 0 52 56 50 661.3 0 50 57 71 661.3 0 71 58 151 661.3 0 151 59 80 661.3 0 80 60 71 661.3 0 71 61 95 661.3 0 95 62 95 661.3 0 95 63 29 661.3 0 29 64 49 661.3 0 49 65 59 661.3 0 59 66 51 661.3 0 51 67 27 661.3 0 27 68 38 661.3 0 38 69 33 661.3 0 33 70 33 661.3 0 33 71 29 661.3 0 29 72 46 661.3 0 46 73 33 661.3 0 33 74 37 661.3 0 37 75 38 661.3 0 38 76 42 661.3 0 42 77 260 661.3 0 260 78 61 661.3 0 61 79 43 661.3 0 43 80 48 661.3 0 48 81 44 661.3 0 44 82 42 661.3 0 42 83 90 661.3 0 90 84 123 661.3 0 123 85 110 661.3 0 110 86 68 661.3 0 68 87 224 661.3 0 224 88 53 661.3 0 53 89 64 661.3 0 64 90 75 661.3 0 75 91 78 661.3 0 78 92 179 661.3 0 179 93 146 661.3 0 146 94 314 661.3 0 314 95 76 661.3 0 76 96 161 661.3 0 161 97 402 661.3 0 402 98 147 661.3 0 147 99 246 661.3 0 246 100 161 661.3 0 161 101 212 661.3 0 212 102 395 661.3 0 395 103 109 661.3 0 109 104 135 661.3 0 135 105 81 661.3 0 81 106 163 661.3 0 163 107 412 661.3 0 412 108 722 661.3 0 722 109 576 661.3 0 576 110 812 661.3 0 812 111 1213 661.3 0 1213 112 2049 661.3 0 2049 113 4728 661.3 0 4728 114 80004 661.3 0 80004 115 12156 661.3 0 12156 116 60686 661.3 0 60686 117 405 661.3 0 405 118 72 661.3 0 72 119 49 661.3 0 49 120 46 661.3 0 46 121 43 661.3 0 43 122 34 661.3 0 34 123 46 661.3 0 46 124 39 661.3 0 39 125 30 661.3 0 30 126 70 661.3 0 70 127 84 661.3 0 84 128 86 661.3 0 86 129 144 661.3 0 144 130 177 661.3 0 177 131 99 661.3 0 99 132 98 661.3 0 98 133 69 661.3 0 69 134 85 661.3 0 85 135 136 661.3 0 136 136 210 661.3 0 210 137 129 661.3 0 129 138 101 661.3 0 101 139 85 661.3 0 85 140 248 661.3 0 248 141 688 661.3 0 688 142 1260 661.3 0 1260 143 440 661.3 0 440 144 224 661.3 0 224 145 395 661.3 0 395 146 842 661.3 0 842 147 15059 661.3 0 15059 148 2532 661.3 0 2532 149 4062 661.3 0 4062 150 175 661.3 0 175 151 213 661.3 0 213 152 392 661.3 0 392 153 5887 661.3 0 5887 154 2114 661.3 0 2114 155 2986 661.3 0 2986 156 416 661.3 0 416 157 212 661.3 0 212 158 185 661.3 0 185 159 48 661.3 0 48 160 76 661.3 0 76 161 61 661.3 0 61 162 94 661.3 0 94 163 76 661.3 0 76 164 77 661.3 0 77 165 60 661.3 0 60 166 75 661.3 0 75 167 95 661.3 0 95 168 156 661.3 0 156 169 485 661.3 0 485 170 270 661.3 0 270 171 207 661.3 0 207 172 42 661.3 0 42 173 50 661.3 0 50 174 44 661.3 0 44 175 66 661.3 0 66 176 91 661.3 0 91 177 58 661.3 0 58 178 68 661.3 0 68 179 59 661.3 0 59 180 48 661.3 0 48 181 124 661.3 0 124 182 115 661.3 0 115 183 181 661.3 0 181 184 88 661.3 0 88 185 112 661.3 0 112 186 119 661.3 0 119 187 61 661.3 0 61 188 60 661.3 0 60 189 48 661.3 0 48 190 77 661.3 0 77 191 63 661.3 0 63 192 57 661.3 0 57 193 58 661.3 0 58 194 47 661.3 0 47 195 45 661.3 0 45 196 42 661.3 0 42 197 46 661.3 0 46 198 56 661.3 0 56 199 35 661.3 0 35 200 44 661.3 0 44 201 46 661.3 0 46 202 270 661.3 0 270 203 234 661.3 0 234 204 227 661.3 0 227 205 60 661.3 0 60 206 49 661.3 0 49 207 38 661.3 0 38 208 43 661.3 0 43 209 51 661.3 0 51 210 48 661.3 0 48 211 43 661.3 0 43 212 52 661.3 0 52 213 76 661.3 0 76 214 53 661.3 0 53 215 70 661.3 0 70 216 187 661.3 0 187 217 147 661.3 0 147 218 140 661.3 0 140 219 44 661.3 0 44 220 39 661.3 0 39 221 41 661.3 0 41 222 38 661.3 0 38 223 50 661.3 0 50 224 52 661.3 0 52 225 65 661.3 0 65 226 271 661.3 0 271 227 179 661.3 0 179 228 144 661.3 0 144 229 42 661.3 0 42 230 49 661.3 0 49 231 46 661.3 0 46 232 44 661.3 0 44 233 55 661.3 0 55 234 68 661.3 0 68 235 76 661.3 0 76 236 73 661.3 0 73 237 70 661.3 0 70 238 41 661.3 0 41 239 29 661.3 0 29 240 35 661.3 0 35 241 31 661.3 0 31 242 42 661.3 0 42 243 41 661.3 0 41 244 73 661.3 0 73 245 78 661.3 0 78 246 68 661.3 0 68 247 44 661.3 0 44 248 30 661.3 0 30 249 42 661.3 0 42 250 46 661.3 0 46 251 67 661.3 0 67 252 39 661.3 0 39 253 79 661.3 0 79 254 125 661.3 0 125 255 116 661.3 0 116 256 70 661.3 0 70 257 51 661.3 0 51 258 28 661.3 0 28 259 29 661.3 0 29 260 40 661.3 0 40 261 34 661.3 0 34 262 47 661.3 0 47 263 59 661.3 0 59 264 62 661.3 0 62 265 50 661.3 0 50 266 48 661.3 0 48 267 74 661.3 0 74 268 63 661.3 0 63 269 58 661.3 0 58 270 89 661.3 0 89 271 87 661.3 0 87 272 76 661.3 0 76 273 172 661.3 0 172 274 133 661.3 0 133 275 239 661.3 0 239 276 73 661.3 0 73 277 73 661.3 0 73 278 59 661.3 0 59 279 118 661.3 0 118 280 128 661.3 0 128 281 507 661.3 0 507 282 496 661.3 0 496 283 396 661.3 0 396 284 78 661.3 0 78 285 111 661.3 0 111 286 97 661.3 0 97 287 105 661.3 0 105 288 34 661.3 0 34 289 41 661.3 0 41 290 177 661.3 0 177 291 186 661.3 0 186 292 159 661.3 0 159 293 109 661.3 0 109 294 78 661.3 0 78 295 74 661.3 0 74 296 103 661.3 0 103 297 44 661.3 0 44 298 57 661.3 0 57 299 38 661.3 0 38 300 16 661.3 0 16 301 21 661.3 0 21 Finished in 8.25 s (37 us/read; 1.61 M reads/minute). === Summary === Total reads processed: 221,502 Reads with adapters: 5,885 (2.7%) Reads that were too short: 10 (0.0%) Reads written (passing filters): 5,875 (2.7%) Total basepairs processed: 40,648,357 bp Total written (filtered): 1,597,721 bp (3.9%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 5885 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 6 0.0 3 0 0 5 0 1 19 67 0.0 3 0 64 1 1 1 20 5767 0.0 4 5487 240 22 7 11 21 21 0.0 4 6 13 2 22 6 0.0 4 0 1 2 0 3 23 3 0.0 4 0 0 0 3 24 1 0.0 4 0 0 0 0 1 28 1 0.0 4 0 0 0 0 1 29 1 0.0 4 0 0 0 0 1 72 1 0.0 4 0 0 0 0 1 100 1 0.0 4 0 0 0 0 1 101 1 0.0 4 0 0 0 0 1 102 1 0.0 4 0 0 0 0 1 104 1 0.0 4 1 131 1 0.0 4 0 0 0 0 1 143 2 0.0 4 0 0 0 0 2 151 1 0.0 4 0 0 0 0 1 157 1 0.0 4 0 0 0 0 1 180 1 0.0 4 0 0 0 0 1 197 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 0.19 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 5,875 Reads with adapters: 1,842 (31.4%) Reads written (passing filters): 5,875 (100.0%) Total basepairs processed: 1,597,721 bp Total written (filtered): 1,173,271 bp (73.4%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 1842 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.1% C: 0.7% G: 12.6% T: 85.7% none/other: 0.0% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "T" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 9 33 0.0 0 3 30 10 150 0.0 1 7 143 11 79 0.0 1 0 79 138 1 0.0 1 1 238 3 0.0 1 3 245 1 0.0 1 1 257 1 0.0 1 1 263 1 0.0 1 1 266 7 0.0 1 7 267 1436 0.0 1 1360 76 268 94 0.0 1 92 2 269 19 0.0 1 18 1 270 17 0.0 1 16 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.