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 172.47 s (50 us/read; 1.21 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 665,115 (19.2%) Reads that were too short: 21,487 (0.6%) Reads written (passing filters): 643,628 (18.5%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 109,019,575 bp (10.4%) === Adapter 1 === Sequence: AGAAGA; Type: regular 5'; Length: 6; Trimmed: 665115 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 2476 847.3 0 2476 7 13378 847.3 0 13378 8 10519 847.3 0 10519 9 193 847.3 0 193 10 288 847.3 0 288 11 122 847.3 0 122 12 118 847.3 0 118 13 94 847.3 0 94 14 89 847.3 0 89 15 116 847.3 0 116 16 79 847.3 0 79 17 72 847.3 0 72 18 87 847.3 0 87 19 94 847.3 0 94 20 88 847.3 0 88 21 84 847.3 0 84 22 84 847.3 0 84 23 106 847.3 0 106 24 132 847.3 0 132 25 229 847.3 0 229 26 161 847.3 0 161 27 147 847.3 0 147 28 109 847.3 0 109 29 92 847.3 0 92 30 107 847.3 0 107 31 66 847.3 0 66 32 63 847.3 0 63 33 81 847.3 0 81 34 87 847.3 0 87 35 111 847.3 0 111 36 131 847.3 0 131 37 125 847.3 0 125 38 80 847.3 0 80 39 84 847.3 0 84 40 162 847.3 0 162 41 72 847.3 0 72 42 116 847.3 0 116 43 128 847.3 0 128 44 89 847.3 0 89 45 90 847.3 0 90 46 84 847.3 0 84 47 75 847.3 0 75 48 81 847.3 0 81 49 90 847.3 0 90 50 81 847.3 0 81 51 93 847.3 0 93 52 78 847.3 0 78 53 154 847.3 0 154 54 87 847.3 0 87 55 109 847.3 0 109 56 119 847.3 0 119 57 92 847.3 0 92 58 95 847.3 0 95 59 70 847.3 0 70 60 100 847.3 0 100 61 155 847.3 0 155 62 137 847.3 0 137 63 145 847.3 0 145 64 111 847.3 0 111 65 123 847.3 0 123 66 117 847.3 0 117 67 124 847.3 0 124 68 147 847.3 0 147 69 151 847.3 0 151 70 169 847.3 0 169 71 131 847.3 0 131 72 583 847.3 0 583 73 348 847.3 0 348 74 1913 847.3 0 1913 75 686 847.3 0 686 76 265 847.3 0 265 77 702 847.3 0 702 78 385 847.3 0 385 79 450 847.3 0 450 80 441 847.3 0 441 81 1824 847.3 0 1824 82 711 847.3 0 711 83 860 847.3 0 860 84 574 847.3 0 574 85 374 847.3 0 374 86 377 847.3 0 377 87 221 847.3 0 221 88 149 847.3 0 149 89 150 847.3 0 150 90 201 847.3 0 201 91 149 847.3 0 149 92 152 847.3 0 152 93 223 847.3 0 223 94 297 847.3 0 297 95 201 847.3 0 201 96 219 847.3 0 219 97 231 847.3 0 231 98 190 847.3 0 190 99 233 847.3 0 233 100 280 847.3 0 280 101 378 847.3 0 378 102 499 847.3 0 499 103 561 847.3 0 561 104 803 847.3 0 803 105 1196 847.3 0 1196 106 471 847.3 0 471 107 556 847.3 0 556 108 1005 847.3 0 1005 109 626 847.3 0 626 110 511 847.3 0 511 111 1086 847.3 0 1086 112 840 847.3 0 840 113 1052 847.3 0 1052 114 969 847.3 0 969 115 1395 847.3 0 1395 116 1952 847.3 0 1952 117 3104 847.3 0 3104 118 51448 847.3 0 51448 119 45974 847.3 0 45974 120 25734 847.3 0 25734 121 5989 847.3 0 5989 122 5625 847.3 0 5625 123 4073 847.3 0 4073 124 602 847.3 0 602 125 606 847.3 0 606 126 1081 847.3 0 1081 127 1030 847.3 0 1030 128 724 847.3 0 724 129 910 847.3 0 910 130 1075 847.3 0 1075 131 1639 847.3 0 1639 132 2615 847.3 0 2615 133 1522 847.3 0 1522 134 1734 847.3 0 1734 135 2053 847.3 0 2053 136 1759 847.3 0 1759 137 2128 847.3 0 2128 138 2988 847.3 0 2988 139 16170 847.3 0 16170 140 27028 847.3 0 27028 141 19626 847.3 0 19626 142 8129 847.3 0 8129 143 4610 847.3 0 4610 144 6726 847.3 0 6726 145 77151 847.3 0 77151 146 70797 847.3 0 70797 147 92827 847.3 0 92827 148 31193 847.3 0 31193 149 16058 847.3 0 16058 150 2116 847.3 0 2116 151 2030 847.3 0 2030 152 1443 847.3 0 1443 153 1263 847.3 0 1263 154 1047 847.3 0 1047 155 753 847.3 0 753 156 371 847.3 0 371 157 550 847.3 0 550 158 486 847.3 0 486 159 1004 847.3 0 1004 160 654 847.3 0 654 161 355 847.3 0 355 162 465 847.3 0 465 163 626 847.3 0 626 164 1049 847.3 0 1049 165 11773 847.3 0 11773 166 9094 847.3 0 9094 167 6010 847.3 0 6010 168 331 847.3 0 331 169 409 847.3 0 409 170 179 847.3 0 179 171 179 847.3 0 179 172 176 847.3 0 176 173 238 847.3 0 238 174 250 847.3 0 250 175 221 847.3 0 221 176 175 847.3 0 175 177 150 847.3 0 150 178 143 847.3 0 143 179 138 847.3 0 138 180 144 847.3 0 144 181 174 847.3 0 174 182 169 847.3 0 169 183 201 847.3 0 201 184 172 847.3 0 172 185 143 847.3 0 143 186 152 847.3 0 152 187 189 847.3 0 189 188 152 847.3 0 152 189 160 847.3 0 160 190 182 847.3 0 182 191 205 847.3 0 205 192 312 847.3 0 312 193 315 847.3 0 315 194 267 847.3 0 267 195 187 847.3 0 187 196 160 847.3 0 160 197 172 847.3 0 172 198 148 847.3 0 148 199 265 847.3 0 265 200 288 847.3 0 288 201 309 847.3 0 309 202 159 847.3 0 159 203 136 847.3 0 136 204 143 847.3 0 143 205 180 847.3 0 180 206 170 847.3 0 170 207 269 847.3 0 269 208 157 847.3 0 157 209 205 847.3 0 205 210 177 847.3 0 177 211 159 847.3 0 159 212 152 847.3 0 152 213 158 847.3 0 158 214 139 847.3 0 139 215 169 847.3 0 169 216 495 847.3 0 495 217 760 847.3 0 760 218 1319 847.3 0 1319 219 1360 847.3 0 1360 220 181 847.3 0 181 221 182 847.3 0 182 222 139 847.3 0 139 223 166 847.3 0 166 224 135 847.3 0 135 225 142 847.3 0 142 226 159 847.3 0 159 227 148 847.3 0 148 228 190 847.3 0 190 229 133 847.3 0 133 230 131 847.3 0 131 231 128 847.3 0 128 232 123 847.3 0 123 233 123 847.3 0 123 234 115 847.3 0 115 235 123 847.3 0 123 236 113 847.3 0 113 237 132 847.3 0 132 238 145 847.3 0 145 239 119 847.3 0 119 240 148 847.3 0 148 241 128 847.3 0 128 242 139 847.3 0 139 243 167 847.3 0 167 244 126 847.3 0 126 245 126 847.3 0 126 246 197 847.3 0 197 247 169 847.3 0 169 248 141 847.3 0 141 249 133 847.3 0 133 250 111 847.3 0 111 251 99 847.3 0 99 252 143 847.3 0 143 253 120 847.3 0 120 254 91 847.3 0 91 255 137 847.3 0 137 256 160 847.3 0 160 257 130 847.3 0 130 258 118 847.3 0 118 259 134 847.3 0 134 260 151 847.3 0 151 261 156 847.3 0 156 262 286 847.3 0 286 263 222 847.3 0 222 264 161 847.3 0 161 265 195 847.3 0 195 266 178 847.3 0 178 267 165 847.3 0 165 268 123 847.3 0 123 269 102 847.3 0 102 270 100 847.3 0 100 271 140 847.3 0 140 272 130 847.3 0 130 273 121 847.3 0 121 274 132 847.3 0 132 275 153 847.3 0 153 276 136 847.3 0 136 277 151 847.3 0 151 278 174 847.3 0 174 279 145 847.3 0 145 280 124 847.3 0 124 281 156 847.3 0 156 282 132 847.3 0 132 283 121 847.3 0 121 284 128 847.3 0 128 285 138 847.3 0 138 286 124 847.3 0 124 287 135 847.3 0 135 288 186 847.3 0 186 289 160 847.3 0 160 290 145 847.3 0 145 291 169 847.3 0 169 292 144 847.3 0 144 293 145 847.3 0 145 294 157 847.3 0 157 295 158 847.3 0 158 296 166 847.3 0 166 297 242 847.3 0 242 298 221 847.3 0 221 299 244 847.3 0 244 300 394 847.3 0 394 301 2926 847.3 0 2926 Finished in 37.91 s (59 us/read; 1.02 M reads/minute). === Summary === Total reads processed: 643,628 Reads with adapters: 13,087 (2.0%) Reads that were too short: 247 (0.0%) Reads written (passing filters): 12,840 (2.0%) Total basepairs processed: 109,019,575 bp Total written (filtered): 3,497,171 bp (3.2%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 13087 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 1 0.0 3 0 0 0 1 18 13 0.0 3 0 0 10 0 3 19 157 0.0 3 0 133 14 6 4 20 10435 0.0 4 9897 441 78 15 4 21 50 0.0 4 23 21 3 2 1 22 28 0.0 4 6 15 4 2 1 23 2085 0.0 4 1961 83 16 18 7 24 7 0.0 4 3 1 1 0 2 25 5 0.0 4 0 1 1 0 3 26 7 0.0 4 0 0 0 6 1 27 2 0.0 4 0 0 0 0 2 29 1 0.0 4 0 0 0 0 1 34 1 0.0 4 0 0 0 1 37 1 0.0 4 0 0 0 0 1 41 4 0.0 4 0 0 0 0 4 42 6 0.0 4 0 0 0 0 6 48 3 0.0 4 0 0 0 1 2 49 1 0.0 4 0 0 0 0 1 50 3 0.0 4 0 0 0 0 3 51 1 0.0 4 0 0 0 0 1 53 13 0.0 4 0 0 0 0 13 54 1 0.0 4 1 55 1 0.0 4 0 0 0 0 1 56 3 0.0 4 0 0 0 1 2 58 1 0.0 4 0 0 0 0 1 66 1 0.0 4 0 0 0 0 1 67 1 0.0 4 0 0 0 0 1 70 1 0.0 4 0 0 0 0 1 71 1 0.0 4 0 0 0 0 1 72 1 0.0 4 0 0 0 0 1 73 1 0.0 4 0 0 0 0 1 74 1 0.0 4 0 0 0 0 1 75 3 0.0 4 0 0 0 0 3 76 4 0.0 4 0 0 0 0 4 77 10 0.0 4 0 0 1 0 9 78 2 0.0 4 0 0 0 0 2 79 3 0.0 4 0 0 0 0 3 80 4 0.0 4 0 0 0 0 4 81 1 0.0 4 0 0 0 0 1 83 1 0.0 4 0 0 0 0 1 85 5 0.0 4 0 0 0 0 5 86 5 0.0 4 0 0 0 0 5 87 4 0.0 4 0 0 0 1 3 88 2 0.0 4 0 0 0 0 2 89 1 0.0 4 0 0 0 0 1 97 3 0.0 4 0 0 0 0 3 98 3 0.0 4 0 0 0 0 3 99 3 0.0 4 0 0 0 0 3 100 14 0.0 4 0 0 0 0 14 101 1 0.0 4 0 0 0 0 1 107 1 0.0 4 0 0 0 0 1 108 1 0.0 4 0 0 0 0 1 109 2 0.0 4 0 0 0 0 2 113 1 0.0 4 0 0 0 0 1 115 1 0.0 4 0 0 0 0 1 116 2 0.0 4 0 0 0 0 2 117 1 0.0 4 0 0 0 0 1 118 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 1 122 2 0.0 4 0 0 0 0 2 124 36 0.0 4 0 0 0 0 36 125 9 0.0 4 0 0 0 0 9 126 27 0.0 4 0 0 0 1 26 127 4 0.0 4 0 0 0 0 4 132 1 0.0 4 0 0 0 0 1 133 1 0.0 4 0 0 0 0 1 135 2 0.0 4 0 0 0 0 2 136 4 0.0 4 0 0 0 0 4 139 1 0.0 4 0 1 143 2 0.0 4 0 0 0 0 2 145 4 0.0 4 0 0 0 0 4 146 1 0.0 4 0 0 0 0 1 148 1 0.0 4 0 0 0 0 1 149 2 0.0 4 0 0 0 0 2 151 2 0.0 4 0 0 0 0 2 152 1 0.0 4 0 0 0 0 1 154 2 0.0 4 0 0 0 0 2 155 14 0.0 4 0 0 0 0 14 156 1 0.0 4 0 0 0 0 1 157 4 0.0 4 0 0 0 0 4 158 2 0.0 4 0 0 0 0 2 159 1 0.0 4 0 0 0 0 1 160 1 0.0 4 0 0 0 0 1 163 1 0.0 4 0 0 0 0 1 164 1 0.0 4 0 0 0 0 1 165 3 0.0 4 0 0 0 0 3 168 2 0.0 4 0 0 0 0 2 171 2 0.0 4 0 0 0 0 2 172 2 0.0 4 0 0 0 0 2 174 2 0.0 4 0 0 0 0 2 177 8 0.0 4 0 0 0 0 8 178 1 0.0 4 0 0 0 0 1 179 3 0.0 4 1 0 0 0 2 180 1 0.0 4 0 0 0 0 1 181 2 0.0 4 0 0 0 0 2 192 1 0.0 4 0 0 0 0 1 194 1 0.0 4 0 0 0 0 1 199 1 0.0 4 0 0 0 0 1 201 1 0.0 4 0 0 0 1 209 1 0.0 4 0 0 0 0 1 210 1 0.0 4 0 0 0 0 1 219 1 0.0 4 0 0 0 0 1 220 1 0.0 4 0 0 0 0 1 225 1 0.0 4 0 0 0 1 228 1 0.0 4 0 0 0 0 1 235 3 0.0 4 0 0 0 0 3 257 1 0.0 4 0 0 0 0 1 275 1 0.0 4 0 0 0 0 1 294 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 0.81 s (63 us/read; 0.95 M reads/minute). === Summary === Total reads processed: 12,840 Reads with adapters: 2,559 (19.9%) Reads written (passing filters): 12,840 (100.0%) Total basepairs processed: 3,497,171 bp Total written (filtered): 3,462,008 bp (99.0%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2559 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.7% C: 5.7% G: 89.9% T: 2.6% 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 14 200.6 0 14 4 2 50.2 0 2 8 2 0.2 0 2 9 361 0.0 0 30 331 10 748 0.0 1 49 699 11 1372 0.0 1 32 1340 12 9 0.0 1 1 8 13 1 0.0 1 0 1 14 6 0.0 1 0 6 19 1 0.0 1 1 151 7 0.0 1 5 2 208 2 0.0 1 1 1 209 8 0.0 1 7 1 224 24 0.0 1 20 4 258 1 0.0 1 1 273 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.