This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AATGAA -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 170.08 s (49 us/read; 1.22 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 364,995 (10.5%) Reads that were too short: 19,456 (0.6%) Reads written (passing filters): 345,539 (10.0%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 95,637,695 bp (9.2%) === Adapter 1 === Sequence: AATGAA; Type: regular 5'; Length: 6; Trimmed: 364995 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1669 847.3 0 1669 7 2702 847.3 0 2702 8 137153 847.3 0 137153 9 151234 847.3 0 151234 10 200 847.3 0 200 11 89 847.3 0 89 12 73 847.3 0 73 13 63 847.3 0 63 14 79 847.3 0 79 15 71 847.3 0 71 16 65 847.3 0 65 17 69 847.3 0 69 18 52 847.3 0 52 19 59 847.3 0 59 20 56 847.3 0 56 21 69 847.3 0 69 22 79 847.3 0 79 23 74 847.3 0 74 24 68 847.3 0 68 25 85 847.3 0 85 26 73 847.3 0 73 27 86 847.3 0 86 28 87 847.3 0 87 29 87 847.3 0 87 30 86 847.3 0 86 31 85 847.3 0 85 32 78 847.3 0 78 33 70 847.3 0 70 34 68 847.3 0 68 35 78 847.3 0 78 36 77 847.3 0 77 37 72 847.3 0 72 38 80 847.3 0 80 39 81 847.3 0 81 40 62 847.3 0 62 41 101 847.3 0 101 42 112 847.3 0 112 43 82 847.3 0 82 44 106 847.3 0 106 45 137 847.3 0 137 46 124 847.3 0 124 47 130 847.3 0 130 48 70 847.3 0 70 49 94 847.3 0 94 50 91 847.3 0 91 51 58 847.3 0 58 52 61 847.3 0 61 53 59 847.3 0 59 54 81 847.3 0 81 55 78 847.3 0 78 56 100 847.3 0 100 57 101 847.3 0 101 58 70 847.3 0 70 59 94 847.3 0 94 60 86 847.3 0 86 61 98 847.3 0 98 62 125 847.3 0 125 63 98 847.3 0 98 64 151 847.3 0 151 65 147 847.3 0 147 66 220 847.3 0 220 67 112 847.3 0 112 68 163 847.3 0 163 69 173 847.3 0 173 70 125 847.3 0 125 71 130 847.3 0 130 72 287 847.3 0 287 73 318 847.3 0 318 74 150 847.3 0 150 75 175 847.3 0 175 76 315 847.3 0 315 77 496 847.3 0 496 78 479 847.3 0 479 79 7484 847.3 0 7484 80 3865 847.3 0 3865 81 3113 847.3 0 3113 82 428 847.3 0 428 83 424 847.3 0 424 84 370 847.3 0 370 85 139 847.3 0 139 86 264 847.3 0 264 87 217 847.3 0 217 88 224 847.3 0 224 89 164 847.3 0 164 90 164 847.3 0 164 91 197 847.3 0 197 92 185 847.3 0 185 93 176 847.3 0 176 94 167 847.3 0 167 95 139 847.3 0 139 96 195 847.3 0 195 97 238 847.3 0 238 98 198 847.3 0 198 99 225 847.3 0 225 100 251 847.3 0 251 101 245 847.3 0 245 102 162 847.3 0 162 103 187 847.3 0 187 104 174 847.3 0 174 105 191 847.3 0 191 106 209 847.3 0 209 107 201 847.3 0 201 108 234 847.3 0 234 109 222 847.3 0 222 110 190 847.3 0 190 111 184 847.3 0 184 112 222 847.3 0 222 113 180 847.3 0 180 114 208 847.3 0 208 115 258 847.3 0 258 116 288 847.3 0 288 117 304 847.3 0 304 118 203 847.3 0 203 119 225 847.3 0 225 120 265 847.3 0 265 121 273 847.3 0 273 122 224 847.3 0 224 123 227 847.3 0 227 124 370 847.3 0 370 125 608 847.3 0 608 126 359 847.3 0 359 127 343 847.3 0 343 128 333 847.3 0 333 129 256 847.3 0 256 130 283 847.3 0 283 131 249 847.3 0 249 132 224 847.3 0 224 133 178 847.3 0 178 134 165 847.3 0 165 135 212 847.3 0 212 136 271 847.3 0 271 137 298 847.3 0 298 138 620 847.3 0 620 139 453 847.3 0 453 140 365 847.3 0 365 141 557 847.3 0 557 142 487 847.3 0 487 143 230 847.3 0 230 144 249 847.3 0 249 145 189 847.3 0 189 146 180 847.3 0 180 147 188 847.3 0 188 148 144 847.3 0 144 149 176 847.3 0 176 150 284 847.3 0 284 151 229 847.3 0 229 152 216 847.3 0 216 153 145 847.3 0 145 154 167 847.3 0 167 155 194 847.3 0 194 156 212 847.3 0 212 157 183 847.3 0 183 158 377 847.3 0 377 159 312 847.3 0 312 160 487 847.3 0 487 161 149 847.3 0 149 162 176 847.3 0 176 163 173 847.3 0 173 164 267 847.3 0 267 165 182 847.3 0 182 166 248 847.3 0 248 167 164 847.3 0 164 168 167 847.3 0 167 169 177 847.3 0 177 170 200 847.3 0 200 171 196 847.3 0 196 172 177 847.3 0 177 173 154 847.3 0 154 174 171 847.3 0 171 175 162 847.3 0 162 176 157 847.3 0 157 177 220 847.3 0 220 178 200 847.3 0 200 179 168 847.3 0 168 180 195 847.3 0 195 181 190 847.3 0 190 182 786 847.3 0 786 183 1036 847.3 0 1036 184 1445 847.3 0 1445 185 184 847.3 0 184 186 148 847.3 0 148 187 161 847.3 0 161 188 153 847.3 0 153 189 175 847.3 0 175 190 151 847.3 0 151 191 163 847.3 0 163 192 155 847.3 0 155 193 167 847.3 0 167 194 173 847.3 0 173 195 189 847.3 0 189 196 154 847.3 0 154 197 186 847.3 0 186 198 195 847.3 0 195 199 170 847.3 0 170 200 189 847.3 0 189 201 194 847.3 0 194 202 169 847.3 0 169 203 188 847.3 0 188 204 181 847.3 0 181 205 208 847.3 0 208 206 188 847.3 0 188 207 197 847.3 0 197 208 230 847.3 0 230 209 233 847.3 0 233 210 197 847.3 0 197 211 217 847.3 0 217 212 197 847.3 0 197 213 186 847.3 0 186 214 164 847.3 0 164 215 186 847.3 0 186 216 183 847.3 0 183 217 159 847.3 0 159 218 164 847.3 0 164 219 165 847.3 0 165 220 157 847.3 0 157 221 171 847.3 0 171 222 190 847.3 0 190 223 184 847.3 0 184 224 193 847.3 0 193 225 186 847.3 0 186 226 230 847.3 0 230 227 271 847.3 0 271 228 217 847.3 0 217 229 158 847.3 0 158 230 148 847.3 0 148 231 215 847.3 0 215 232 190 847.3 0 190 233 183 847.3 0 183 234 166 847.3 0 166 235 211 847.3 0 211 236 183 847.3 0 183 237 246 847.3 0 246 238 213 847.3 0 213 239 183 847.3 0 183 240 167 847.3 0 167 241 175 847.3 0 175 242 185 847.3 0 185 243 172 847.3 0 172 244 157 847.3 0 157 245 133 847.3 0 133 246 205 847.3 0 205 247 206 847.3 0 206 248 171 847.3 0 171 249 178 847.3 0 178 250 160 847.3 0 160 251 148 847.3 0 148 252 180 847.3 0 180 253 329 847.3 0 329 254 583 847.3 0 583 255 976 847.3 0 976 256 849 847.3 0 849 257 169 847.3 0 169 258 139 847.3 0 139 259 178 847.3 0 178 260 170 847.3 0 170 261 168 847.3 0 168 262 185 847.3 0 185 263 161 847.3 0 161 264 227 847.3 0 227 265 170 847.3 0 170 266 154 847.3 0 154 267 117 847.3 0 117 268 157 847.3 0 157 269 139 847.3 0 139 270 136 847.3 0 136 271 149 847.3 0 149 272 158 847.3 0 158 273 154 847.3 0 154 274 158 847.3 0 158 275 170 847.3 0 170 276 172 847.3 0 172 277 175 847.3 0 175 278 135 847.3 0 135 279 156 847.3 0 156 280 183 847.3 0 183 281 151 847.3 0 151 282 138 847.3 0 138 283 151 847.3 0 151 284 174 847.3 0 174 285 161 847.3 0 161 286 171 847.3 0 171 287 179 847.3 0 179 288 149 847.3 0 149 289 162 847.3 0 162 290 185 847.3 0 185 291 135 847.3 0 135 292 146 847.3 0 146 293 135 847.3 0 135 294 151 847.3 0 151 295 139 847.3 0 139 296 126 847.3 0 126 297 145 847.3 0 145 298 155 847.3 0 155 299 154 847.3 0 154 300 151 847.3 0 151 301 237 847.3 0 237 Finished in 25.18 s (73 us/read; 0.82 M reads/minute). === Summary === Total reads processed: 345,539 Reads with adapters: 136,032 (39.4%) Reads that were too short: 82 (0.0%) Reads written (passing filters): 135,950 (39.3%) Total basepairs processed: 95,637,695 bp Total written (filtered): 37,514,615 bp (39.2%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 136032 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 7 0.0 2 0 0 0 7 15 31 0.0 3 0 0 31 16 652 0.0 3 0 639 13 17 134737 0.0 3 132273 2370 80 14 18 291 0.0 3 27 255 9 19 52 0.0 3 4 0 46 2 20 113 0.0 3 0 1 0 112 21 3 0.0 3 1 0 0 2 22 1 0.0 3 1 24 1 0.0 3 1 25 1 0.0 3 0 0 0 1 26 2 0.0 3 2 28 3 0.0 3 0 0 0 3 32 1 0.0 3 0 0 0 1 36 1 0.0 3 0 0 0 1 40 1 0.0 3 0 0 0 1 41 3 0.0 3 0 0 0 3 43 1 0.0 3 0 0 0 1 44 2 0.0 3 0 0 0 2 50 3 0.0 3 0 0 0 3 51 2 0.0 3 0 0 0 2 53 1 0.0 3 0 0 0 1 57 3 0.0 3 0 0 0 3 58 1 0.0 3 0 0 1 60 1 0.0 3 0 0 0 1 62 1 0.0 3 0 0 0 1 64 2 0.0 3 0 0 0 2 65 2 0.0 3 0 0 0 2 72 1 0.0 3 0 0 0 1 75 1 0.0 3 0 0 0 1 77 1 0.0 3 0 0 0 1 84 1 0.0 3 0 0 0 1 87 1 0.0 3 0 0 0 1 94 1 0.0 3 0 0 0 1 99 1 0.0 3 0 0 0 1 100 1 0.0 3 0 0 0 1 101 1 0.0 3 0 0 0 1 104 1 0.0 3 0 0 0 1 109 3 0.0 3 0 0 0 3 112 12 0.0 3 0 0 0 12 114 1 0.0 3 0 0 1 119 1 0.0 3 0 0 0 1 124 1 0.0 3 0 0 0 1 128 1 0.0 3 0 0 1 129 2 0.0 3 0 0 0 2 134 5 0.0 3 0 0 0 5 136 7 0.0 3 0 0 1 6 140 1 0.0 3 0 0 0 1 141 1 0.0 3 0 0 0 1 145 2 0.0 3 0 0 0 2 147 2 0.0 3 0 0 0 2 150 1 0.0 3 0 0 0 1 158 8 0.0 3 0 0 0 8 160 1 0.0 3 0 0 0 1 170 1 0.0 3 1 172 8 0.0 3 0 0 1 7 175 1 0.0 3 1 179 1 0.0 3 0 0 0 1 180 1 0.0 3 0 0 0 1 183 3 0.0 3 0 0 0 3 186 1 0.0 3 0 0 0 1 192 6 0.0 3 0 0 0 6 214 8 0.0 3 0 0 1 7 216 1 0.0 3 0 0 0 1 218 1 0.0 3 0 0 0 1 221 1 0.0 3 0 0 0 1 225 1 0.0 3 0 0 0 1 238 3 0.0 3 0 0 0 3 248 1 0.0 3 0 0 0 1 279 1 0.0 3 0 0 0 1 280 5 0.0 3 0 0 0 5 281 4 0.0 3 0 0 0 4 282 1 0.0 3 0 0 0 1 283 3 0.0 3 0 0 0 3 287 1 0.0 3 0 0 0 1 292 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 8.15 s (60 us/read; 1.00 M reads/minute). === Summary === Total reads processed: 135,950 Reads with adapters: 6,254 (4.6%) Reads written (passing filters): 135,950 (100.0%) Total basepairs processed: 37,514,615 bp Total written (filtered): 37,495,551 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 6254 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 90.5% C: 5.1% G: 3.7% T: 0.7% 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 5968 2124.2 0 5968 4 273 531.1 0 273 5 10 132.8 0 10 6 3 33.2 0 3 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.