This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGAAGA -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 173.56 s (50 us/read; 1.20 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 645,852 (18.6%) Reads that were too short: 23,798 (0.7%) Reads written (passing filters): 622,054 (17.9%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 105,350,041 bp (10.1%) === Adapter 1 === Sequence: AGAAGA; Type: regular 5'; Length: 6; Trimmed: 645852 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 2612 847.3 0 2612 7 11637 847.3 0 11637 8 12986 847.3 0 12986 9 180 847.3 0 180 10 106 847.3 0 106 11 112 847.3 0 112 12 108 847.3 0 108 13 87 847.3 0 87 14 94 847.3 0 94 15 99 847.3 0 99 16 95 847.3 0 95 17 89 847.3 0 89 18 109 847.3 0 109 19 76 847.3 0 76 20 65 847.3 0 65 21 72 847.3 0 72 22 81 847.3 0 81 23 107 847.3 0 107 24 86 847.3 0 86 25 139 847.3 0 139 26 163 847.3 0 163 27 114 847.3 0 114 28 126 847.3 0 126 29 107 847.3 0 107 30 181 847.3 0 181 31 81 847.3 0 81 32 77 847.3 0 77 33 76 847.3 0 76 34 105 847.3 0 105 35 123 847.3 0 123 36 127 847.3 0 127 37 145 847.3 0 145 38 92 847.3 0 92 39 102 847.3 0 102 40 174 847.3 0 174 41 85 847.3 0 85 42 137 847.3 0 137 43 135 847.3 0 135 44 93 847.3 0 93 45 87 847.3 0 87 46 75 847.3 0 75 47 94 847.3 0 94 48 97 847.3 0 97 49 89 847.3 0 89 50 92 847.3 0 92 51 99 847.3 0 99 52 89 847.3 0 89 53 158 847.3 0 158 54 124 847.3 0 124 55 127 847.3 0 127 56 147 847.3 0 147 57 103 847.3 0 103 58 124 847.3 0 124 59 90 847.3 0 90 60 125 847.3 0 125 61 143 847.3 0 143 62 119 847.3 0 119 63 137 847.3 0 137 64 114 847.3 0 114 65 90 847.3 0 90 66 116 847.3 0 116 67 120 847.3 0 120 68 126 847.3 0 126 69 149 847.3 0 149 70 178 847.3 0 178 71 115 847.3 0 115 72 94 847.3 0 94 73 106 847.3 0 106 74 125 847.3 0 125 75 284 847.3 0 284 76 137 847.3 0 137 77 227 847.3 0 227 78 328 847.3 0 328 79 537 847.3 0 537 80 425 847.3 0 425 81 1496 847.3 0 1496 82 720 847.3 0 720 83 720 847.3 0 720 84 518 847.3 0 518 85 548 847.3 0 548 86 492 847.3 0 492 87 203 847.3 0 203 88 263 847.3 0 263 89 281 847.3 0 281 90 212 847.3 0 212 91 165 847.3 0 165 92 267 847.3 0 267 93 259 847.3 0 259 94 279 847.3 0 279 95 282 847.3 0 282 96 235 847.3 0 235 97 207 847.3 0 207 98 273 847.3 0 273 99 284 847.3 0 284 100 294 847.3 0 294 101 454 847.3 0 454 102 540 847.3 0 540 103 580 847.3 0 580 104 830 847.3 0 830 105 1295 847.3 0 1295 106 486 847.3 0 486 107 595 847.3 0 595 108 1051 847.3 0 1051 109 648 847.3 0 648 110 564 847.3 0 564 111 1055 847.3 0 1055 112 838 847.3 0 838 113 852 847.3 0 852 114 864 847.3 0 864 115 1188 847.3 0 1188 116 1589 847.3 0 1589 117 2256 847.3 0 2256 118 50705 847.3 0 50705 119 45470 847.3 0 45470 120 25128 847.3 0 25128 121 5313 847.3 0 5313 122 5075 847.3 0 5075 123 3308 847.3 0 3308 124 546 847.3 0 546 125 574 847.3 0 574 126 1051 847.3 0 1051 127 995 847.3 0 995 128 750 847.3 0 750 129 879 847.3 0 879 130 1116 847.3 0 1116 131 1473 847.3 0 1473 132 2386 847.3 0 2386 133 1401 847.3 0 1401 134 1573 847.3 0 1573 135 1806 847.3 0 1806 136 1503 847.3 0 1503 137 1821 847.3 0 1821 138 2641 847.3 0 2641 139 16449 847.3 0 16449 140 27209 847.3 0 27209 141 19752 847.3 0 19752 142 7351 847.3 0 7351 143 3723 847.3 0 3723 144 5473 847.3 0 5473 145 79719 847.3 0 79719 146 71073 847.3 0 71073 147 84334 847.3 0 84334 148 27060 847.3 0 27060 149 13398 847.3 0 13398 150 1882 847.3 0 1882 151 1894 847.3 0 1894 152 1445 847.3 0 1445 153 1480 847.3 0 1480 154 1288 847.3 0 1288 155 946 847.3 0 946 156 418 847.3 0 418 157 646 847.3 0 646 158 598 847.3 0 598 159 1070 847.3 0 1070 160 606 847.3 0 606 161 332 847.3 0 332 162 395 847.3 0 395 163 502 847.3 0 502 164 882 847.3 0 882 165 12779 847.3 0 12779 166 9615 847.3 0 9615 167 6216 847.3 0 6216 168 274 847.3 0 274 169 423 847.3 0 423 170 198 847.3 0 198 171 188 847.3 0 188 172 223 847.3 0 223 173 211 847.3 0 211 174 265 847.3 0 265 175 249 847.3 0 249 176 203 847.3 0 203 177 178 847.3 0 178 178 166 847.3 0 166 179 160 847.3 0 160 180 171 847.3 0 171 181 181 847.3 0 181 182 195 847.3 0 195 183 237 847.3 0 237 184 161 847.3 0 161 185 185 847.3 0 185 186 174 847.3 0 174 187 159 847.3 0 159 188 194 847.3 0 194 189 225 847.3 0 225 190 227 847.3 0 227 191 209 847.3 0 209 192 245 847.3 0 245 193 241 847.3 0 241 194 305 847.3 0 305 195 186 847.3 0 186 196 204 847.3 0 204 197 236 847.3 0 236 198 206 847.3 0 206 199 329 847.3 0 329 200 338 847.3 0 338 201 403 847.3 0 403 202 193 847.3 0 193 203 164 847.3 0 164 204 206 847.3 0 206 205 186 847.3 0 186 206 213 847.3 0 213 207 306 847.3 0 306 208 206 847.3 0 206 209 257 847.3 0 257 210 212 847.3 0 212 211 182 847.3 0 182 212 198 847.3 0 198 213 178 847.3 0 178 214 187 847.3 0 187 215 172 847.3 0 172 216 597 847.3 0 597 217 746 847.3 0 746 218 1202 847.3 0 1202 219 1217 847.3 0 1217 220 245 847.3 0 245 221 208 847.3 0 208 222 170 847.3 0 170 223 174 847.3 0 174 224 159 847.3 0 159 225 159 847.3 0 159 226 177 847.3 0 177 227 179 847.3 0 179 228 195 847.3 0 195 229 146 847.3 0 146 230 147 847.3 0 147 231 157 847.3 0 157 232 152 847.3 0 152 233 140 847.3 0 140 234 157 847.3 0 157 235 150 847.3 0 150 236 120 847.3 0 120 237 177 847.3 0 177 238 154 847.3 0 154 239 200 847.3 0 200 240 186 847.3 0 186 241 178 847.3 0 178 242 146 847.3 0 146 243 153 847.3 0 153 244 153 847.3 0 153 245 143 847.3 0 143 246 195 847.3 0 195 247 172 847.3 0 172 248 166 847.3 0 166 249 149 847.3 0 149 250 160 847.3 0 160 251 127 847.3 0 127 252 141 847.3 0 141 253 152 847.3 0 152 254 127 847.3 0 127 255 136 847.3 0 136 256 151 847.3 0 151 257 164 847.3 0 164 258 148 847.3 0 148 259 161 847.3 0 161 260 179 847.3 0 179 261 190 847.3 0 190 262 253 847.3 0 253 263 199 847.3 0 199 264 165 847.3 0 165 265 177 847.3 0 177 266 209 847.3 0 209 267 192 847.3 0 192 268 144 847.3 0 144 269 133 847.3 0 133 270 132 847.3 0 132 271 161 847.3 0 161 272 135 847.3 0 135 273 151 847.3 0 151 274 143 847.3 0 143 275 159 847.3 0 159 276 137 847.3 0 137 277 139 847.3 0 139 278 155 847.3 0 155 279 159 847.3 0 159 280 121 847.3 0 121 281 154 847.3 0 154 282 168 847.3 0 168 283 133 847.3 0 133 284 151 847.3 0 151 285 159 847.3 0 159 286 152 847.3 0 152 287 186 847.3 0 186 288 207 847.3 0 207 289 166 847.3 0 166 290 210 847.3 0 210 291 185 847.3 0 185 292 169 847.3 0 169 293 191 847.3 0 191 294 185 847.3 0 185 295 206 847.3 0 206 296 206 847.3 0 206 297 265 847.3 0 265 298 233 847.3 0 233 299 287 847.3 0 287 300 371 847.3 0 371 301 3285 847.3 0 3285 Finished in 37.00 s (59 us/read; 1.01 M reads/minute). === Summary === Total reads processed: 622,054 Reads with adapters: 15,606 (2.5%) Reads that were too short: 100 (0.0%) Reads written (passing filters): 15,506 (2.5%) Total basepairs processed: 105,350,041 bp Total written (filtered): 4,226,130 bp (4.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 15606 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 2 0.0 3 0 0 0 0 2 18 11 0.0 3 0 0 9 2 19 204 0.0 3 0 201 1 1 1 20 12815 0.0 4 12618 185 4 5 3 21 49 0.0 4 24 24 1 22 40 0.0 4 5 23 6 3 3 23 2341 0.0 4 2291 40 1 9 24 4 0.0 4 3 0 0 0 1 25 1 0.0 4 0 0 1 26 2 0.0 4 0 0 0 2 27 1 0.0 4 0 0 0 0 1 33 1 0.0 4 0 0 0 0 1 35 1 0.0 4 1 41 4 0.0 4 0 0 0 0 4 42 1 0.0 4 0 0 0 0 1 48 1 0.0 4 0 0 0 0 1 50 5 0.0 4 0 0 0 0 5 53 13 0.0 4 0 0 0 0 13 56 1 0.0 4 0 0 0 0 1 58 1 0.0 4 0 0 0 0 1 73 1 0.0 4 0 0 0 0 1 75 2 0.0 4 0 0 0 0 2 76 3 0.0 4 0 0 0 0 3 77 2 0.0 4 0 0 0 0 2 78 1 0.0 4 0 0 0 0 1 79 3 0.0 4 0 0 0 0 3 80 1 0.0 4 1 85 3 0.0 4 1 0 0 1 1 86 2 0.0 4 0 0 0 0 2 97 3 0.0 4 0 0 0 0 3 98 1 0.0 4 0 0 0 0 1 100 5 0.0 4 0 0 0 0 5 101 1 0.0 4 0 0 0 0 1 105 1 0.0 4 0 0 0 0 1 106 1 0.0 4 0 0 0 1 107 2 0.0 4 0 0 0 0 2 108 1 0.0 4 0 0 0 0 1 113 1 0.0 4 0 0 0 0 1 117 2 0.0 4 0 1 0 0 1 119 1 0.0 4 0 0 0 0 1 120 1 0.0 4 0 0 0 0 1 121 1 0.0 4 0 0 0 0 1 123 1 0.0 4 0 0 0 0 1 124 10 0.0 4 0 0 0 1 9 125 5 0.0 4 0 0 0 1 4 126 20 0.0 4 0 0 0 0 20 127 1 0.0 4 0 0 0 0 1 129 2 0.0 4 1 0 0 0 1 138 1 0.0 4 0 1 143 3 0.0 4 0 0 0 0 3 144 1 0.0 4 1 145 2 0.0 4 0 0 0 0 2 150 1 0.0 4 0 0 0 0 1 155 6 0.0 4 0 0 0 0 6 156 1 0.0 4 0 0 0 0 1 159 1 0.0 4 0 0 0 0 1 164 2 0.0 4 0 0 0 0 2 165 1 0.0 4 0 0 0 0 1 171 1 0.0 4 0 0 0 0 1 176 2 0.0 4 2 177 2 0.0 4 0 1 0 0 1 178 1 0.0 4 0 1 187 1 0.0 4 0 0 0 0 1 200 1 0.0 4 0 0 0 0 1 218 1 0.0 4 0 0 0 0 1 235 1 0.0 4 0 0 0 0 1 291 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 0.90 s (58 us/read; 1.03 M reads/minute). === Summary === Total reads processed: 15,506 Reads with adapters: 1,456 (9.4%) Reads written (passing filters): 15,506 (100.0%) Total basepairs processed: 4,226,130 bp Total written (filtered): 4,205,837 bp (99.5%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 1456 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.4% C: 2.1% G: 94.0% T: 2.4% 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 8 242.3 0 8 4 1 60.6 0 1 5 1 15.1 0 1 6 1 3.8 0 1 8 1 0.2 0 1 9 446 0.1 0 14 432 10 379 0.0 1 14 365 11 585 0.0 1 3 582 12 4 0.0 1 1 3 19 2 0.0 1 1 1 20 1 0.0 1 1 151 2 0.0 1 0 2 209 2 0.0 1 1 1 224 20 0.0 1 18 2 225 2 0.0 1 2 251 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.