This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TGGCGG -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 162.91 s (47 us/read; 1.28 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 73,650 (2.1%) Reads that were too short: 25,371 (0.7%) Reads written (passing filters): 48,279 (1.4%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 12,044,473 bp (1.2%) === Adapter 1 === Sequence: TGGCGG; Type: regular 5'; Length: 6; Trimmed: 73650 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1062 847.3 0 1062 7 13216 847.3 0 13216 8 368 847.3 0 368 9 12447 847.3 0 12447 10 103 847.3 0 103 11 67 847.3 0 67 12 84 847.3 0 84 13 91 847.3 0 91 14 100 847.3 0 100 15 74 847.3 0 74 16 52 847.3 0 52 17 83 847.3 0 83 18 125 847.3 0 125 19 86 847.3 0 86 20 71 847.3 0 71 21 61 847.3 0 61 22 77 847.3 0 77 23 62 847.3 0 62 24 61 847.3 0 61 25 64 847.3 0 64 26 60 847.3 0 60 27 62 847.3 0 62 28 69 847.3 0 69 29 67 847.3 0 67 30 90 847.3 0 90 31 62 847.3 0 62 32 74 847.3 0 74 33 72 847.3 0 72 34 70 847.3 0 70 35 79 847.3 0 79 36 80 847.3 0 80 37 107 847.3 0 107 38 97 847.3 0 97 39 107 847.3 0 107 40 75 847.3 0 75 41 86 847.3 0 86 42 71 847.3 0 71 43 83 847.3 0 83 44 94 847.3 0 94 45 82 847.3 0 82 46 97 847.3 0 97 47 386 847.3 0 386 48 297 847.3 0 297 49 215 847.3 0 215 50 106 847.3 0 106 51 86 847.3 0 86 52 172 847.3 0 172 53 75 847.3 0 75 54 103 847.3 0 103 55 98 847.3 0 98 56 81 847.3 0 81 57 58 847.3 0 58 58 106 847.3 0 106 59 182 847.3 0 182 60 201 847.3 0 201 61 144 847.3 0 144 62 131 847.3 0 131 63 92 847.3 0 92 64 64 847.3 0 64 65 63 847.3 0 63 66 75 847.3 0 75 67 77 847.3 0 77 68 71 847.3 0 71 69 96 847.3 0 96 70 87 847.3 0 87 71 71 847.3 0 71 72 97 847.3 0 97 73 78 847.3 0 78 74 73 847.3 0 73 75 70 847.3 0 70 76 113 847.3 0 113 77 169 847.3 0 169 78 121 847.3 0 121 79 104 847.3 0 104 80 141 847.3 0 141 81 72 847.3 0 72 82 78 847.3 0 78 83 91 847.3 0 91 84 378 847.3 0 378 85 340 847.3 0 340 86 214 847.3 0 214 87 79 847.3 0 79 88 59 847.3 0 59 89 65 847.3 0 65 90 72 847.3 0 72 91 94 847.3 0 94 92 67 847.3 0 67 93 68 847.3 0 68 94 91 847.3 0 91 95 69 847.3 0 69 96 75 847.3 0 75 97 70 847.3 0 70 98 57 847.3 0 57 99 85 847.3 0 85 100 49 847.3 0 49 101 69 847.3 0 69 102 79 847.3 0 79 103 70 847.3 0 70 104 67 847.3 0 67 105 73 847.3 0 73 106 88 847.3 0 88 107 70 847.3 0 70 108 65 847.3 0 65 109 77 847.3 0 77 110 77 847.3 0 77 111 80 847.3 0 80 112 365 847.3 0 365 113 589 847.3 0 589 114 173 847.3 0 173 115 78 847.3 0 78 116 64 847.3 0 64 117 81 847.3 0 81 118 66 847.3 0 66 119 91 847.3 0 91 120 70 847.3 0 70 121 86 847.3 0 86 122 58 847.3 0 58 123 75 847.3 0 75 124 74 847.3 0 74 125 73 847.3 0 73 126 72 847.3 0 72 127 152 847.3 0 152 128 142 847.3 0 142 129 113 847.3 0 113 130 130 847.3 0 130 131 98 847.3 0 98 132 256 847.3 0 256 133 357 847.3 0 357 134 434 847.3 0 434 135 216 847.3 0 216 136 136 847.3 0 136 137 83 847.3 0 83 138 87 847.3 0 87 139 88 847.3 0 88 140 110 847.3 0 110 141 670 847.3 0 670 142 359 847.3 0 359 143 299 847.3 0 299 144 78 847.3 0 78 145 72 847.3 0 72 146 82 847.3 0 82 147 84 847.3 0 84 148 137 847.3 0 137 149 81 847.3 0 81 150 64 847.3 0 64 151 99 847.3 0 99 152 314 847.3 0 314 153 316 847.3 0 316 154 246 847.3 0 246 155 119 847.3 0 119 156 68 847.3 0 68 157 82 847.3 0 82 158 75 847.3 0 75 159 66 847.3 0 66 160 63 847.3 0 63 161 90 847.3 0 90 162 79 847.3 0 79 163 89 847.3 0 89 164 82 847.3 0 82 165 72 847.3 0 72 166 104 847.3 0 104 167 90 847.3 0 90 168 68 847.3 0 68 169 97 847.3 0 97 170 88 847.3 0 88 171 77 847.3 0 77 172 86 847.3 0 86 173 100 847.3 0 100 174 73 847.3 0 73 175 76 847.3 0 76 176 67 847.3 0 67 177 72 847.3 0 72 178 75 847.3 0 75 179 53 847.3 0 53 180 64 847.3 0 64 181 69 847.3 0 69 182 75 847.3 0 75 183 79 847.3 0 79 184 97 847.3 0 97 185 72 847.3 0 72 186 84 847.3 0 84 187 175 847.3 0 175 188 67 847.3 0 67 189 91 847.3 0 91 190 76 847.3 0 76 191 81 847.3 0 81 192 92 847.3 0 92 193 84 847.3 0 84 194 62 847.3 0 62 195 66 847.3 0 66 196 75 847.3 0 75 197 78 847.3 0 78 198 78 847.3 0 78 199 76 847.3 0 76 200 69 847.3 0 69 201 111 847.3 0 111 202 121 847.3 0 121 203 279 847.3 0 279 204 76 847.3 0 76 205 87 847.3 0 87 206 70 847.3 0 70 207 76 847.3 0 76 208 56 847.3 0 56 209 73 847.3 0 73 210 56 847.3 0 56 211 93 847.3 0 93 212 92 847.3 0 92 213 141 847.3 0 141 214 98 847.3 0 98 215 82 847.3 0 82 216 104 847.3 0 104 217 104 847.3 0 104 218 106 847.3 0 106 219 105 847.3 0 105 220 106 847.3 0 106 221 69 847.3 0 69 222 56 847.3 0 56 223 53 847.3 0 53 224 86 847.3 0 86 225 84 847.3 0 84 226 73 847.3 0 73 227 77 847.3 0 77 228 66 847.3 0 66 229 152 847.3 0 152 230 286 847.3 0 286 231 140 847.3 0 140 232 71 847.3 0 71 233 59 847.3 0 59 234 88 847.3 0 88 235 394 847.3 0 394 236 367 847.3 0 367 237 353 847.3 0 353 238 162 847.3 0 162 239 108 847.3 0 108 240 68 847.3 0 68 241 62 847.3 0 62 242 61 847.3 0 61 243 57 847.3 0 57 244 89 847.3 0 89 245 145 847.3 0 145 246 219 847.3 0 219 247 180 847.3 0 180 248 143 847.3 0 143 249 93 847.3 0 93 250 93 847.3 0 93 251 75 847.3 0 75 252 119 847.3 0 119 253 105 847.3 0 105 254 95 847.3 0 95 255 373 847.3 0 373 256 553 847.3 0 553 257 497 847.3 0 497 258 162 847.3 0 162 259 65 847.3 0 65 260 119 847.3 0 119 261 145 847.3 0 145 262 114 847.3 0 114 263 81 847.3 0 81 264 73 847.3 0 73 265 63 847.3 0 63 266 62 847.3 0 62 267 57 847.3 0 57 268 68 847.3 0 68 269 74 847.3 0 74 270 72 847.3 0 72 271 81 847.3 0 81 272 113 847.3 0 113 273 716 847.3 0 716 274 482 847.3 0 482 275 175 847.3 0 175 276 287 847.3 0 287 277 68 847.3 0 68 278 96 847.3 0 96 279 76 847.3 0 76 280 102 847.3 0 102 281 97 847.3 0 97 282 91 847.3 0 91 283 164 847.3 0 164 284 256 847.3 0 256 285 322 847.3 0 322 286 258 847.3 0 258 287 251 847.3 0 251 288 223 847.3 0 223 289 185 847.3 0 185 290 131 847.3 0 131 291 147 847.3 0 147 292 137 847.3 0 137 293 140 847.3 0 140 294 195 847.3 0 195 295 163 847.3 0 163 296 276 847.3 0 276 297 358 847.3 0 358 298 4771 847.3 0 4771 299 3618 847.3 0 3618 300 2262 847.3 0 2262 301 279 847.3 0 279 Finished in 3.31 s (69 us/read; 0.88 M reads/minute). === Summary === Total reads processed: 48,279 Reads with adapters: 12,981 (26.9%) Reads that were too short: 61 (0.1%) Reads written (passing filters): 12,920 (26.8%) Total basepairs processed: 12,044,473 bp Total written (filtered): 3,535,170 bp (29.4%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 12981 times. No. of allowed errors: 0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-17 bp: 3 Overview of removed sequences length count expect max.err error counts 14 1 0.0 2 0 0 0 1 15 6 0.0 3 0 0 6 16 89 0.0 3 0 85 4 17 12630 0.0 3 12342 270 17 1 18 36 0.0 3 4 26 3 3 19 10 0.0 3 1 0 6 3 20 27 0.0 3 1 0 0 26 23 1 0.0 3 0 0 0 1 38 2 0.0 3 0 0 0 2 39 17 0.0 3 0 0 0 17 42 2 0.0 3 0 0 2 48 2 0.0 3 0 0 0 2 49 1 0.0 3 0 0 0 1 50 11 0.0 3 0 0 0 11 53 2 0.0 3 0 0 0 2 59 1 0.0 3 0 0 0 1 79 12 0.0 3 0 0 0 12 82 2 0.0 3 0 0 0 2 87 2 0.0 3 0 0 0 2 88 3 0.0 3 0 0 0 3 90 2 0.0 3 0 0 0 2 95 1 0.0 3 0 0 0 1 99 1 0.0 3 1 100 1 0.0 3 0 0 0 1 101 52 0.0 3 0 0 0 52 102 2 0.0 3 0 0 0 2 103 1 0.0 3 0 0 0 1 108 1 0.0 3 0 0 0 1 119 2 0.0 3 0 0 0 2 122 1 0.0 3 0 0 0 1 123 2 0.0 3 0 0 0 2 132 1 0.0 3 0 0 0 1 133 1 0.0 3 0 0 0 1 143 28 0.0 3 0 0 0 28 144 1 0.0 3 0 0 0 1 145 5 0.0 3 0 0 0 5 152 1 0.0 3 0 0 0 1 154 4 0.0 3 0 0 0 4 160 1 0.0 3 0 0 0 1 174 1 0.0 3 0 0 0 1 175 2 0.0 3 0 0 0 2 179 1 0.0 3 0 0 0 1 181 1 0.0 3 0 0 0 1 182 1 0.0 3 0 0 0 1 192 1 0.0 3 0 0 0 1 195 1 0.0 3 0 0 0 1 199 1 0.0 3 0 0 0 1 200 1 0.0 3 0 0 0 1 203 1 0.0 3 0 0 0 1 205 1 0.0 3 0 0 0 1 208 1 0.0 3 0 0 0 1 280 1 0.0 3 0 0 0 1 283 1 0.0 3 0 0 0 1 293 1 0.0 3 0 0 0 1 This is cutadapt 1.11 with Python 2.7.12 Command line parameters: -a taatctatgggnncatcagg - Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.78 s (60 us/read; 0.99 M reads/minute). === Summary === Total reads processed: 12,920 Reads with adapters: 976 (7.6%) Reads written (passing filters): 12,920 (100.0%) Total basepairs processed: 3,535,170 bp Total written (filtered): 3,532,225 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 976 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 87.3% C: 4.8% G: 7.7% T: 0.2% none/other: 0.0% WARNING: The adapter is preceded by "A" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "A" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 3 959 201.9 0 959 4 17 50.5 0 17 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.