This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g GGCGCA -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 170.45 s (49 us/read; 1.22 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 540,958 (15.6%) Reads that were too short: 20,468 (0.6%) Reads written (passing filters): 520,490 (15.0%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 128,627,688 bp (12.3%) === Adapter 1 === Sequence: GGCGCA; Type: regular 5'; Length: 6; Trimmed: 540958 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 453 847.3 0 453 7 4609 847.3 0 4609 8 4958 847.3 0 4958 9 307 847.3 0 307 10 412 847.3 0 412 11 260 847.3 0 260 12 215 847.3 0 215 13 656 847.3 0 656 14 581 847.3 0 581 15 533 847.3 0 533 16 438 847.3 0 438 17 604 847.3 0 604 18 894 847.3 0 894 19 1387 847.3 0 1387 20 39292 847.3 0 39292 21 34257 847.3 0 34257 22 24083 847.3 0 24083 23 298 847.3 0 298 24 203 847.3 0 203 25 337 847.3 0 337 26 205 847.3 0 205 27 167 847.3 0 167 28 126 847.3 0 126 29 271 847.3 0 271 30 185 847.3 0 185 31 316 847.3 0 316 32 477 847.3 0 477 33 837 847.3 0 837 34 843 847.3 0 843 35 1649 847.3 0 1649 36 2721 847.3 0 2721 37 736 847.3 0 736 38 917 847.3 0 917 39 1711 847.3 0 1711 40 1024 847.3 0 1024 41 905 847.3 0 905 42 1779 847.3 0 1779 43 1297 847.3 0 1297 44 1590 847.3 0 1590 45 1423 847.3 0 1423 46 2046 847.3 0 2046 47 3175 847.3 0 3175 48 5473 847.3 0 5473 49 141199 847.3 0 141199 50 125491 847.3 0 125491 51 62591 847.3 0 62591 52 275 847.3 0 275 53 71 847.3 0 71 54 61 847.3 0 61 55 57 847.3 0 57 56 63 847.3 0 63 57 63 847.3 0 63 58 78 847.3 0 78 59 70 847.3 0 70 60 78 847.3 0 78 61 55 847.3 0 55 62 81 847.3 0 81 63 505 847.3 0 505 64 458 847.3 0 458 65 362 847.3 0 362 66 40 847.3 0 40 67 55 847.3 0 55 68 49 847.3 0 49 69 42 847.3 0 42 70 63 847.3 0 63 71 55 847.3 0 55 72 36 847.3 0 36 73 55 847.3 0 55 74 48 847.3 0 48 75 50 847.3 0 50 76 62 847.3 0 62 77 52 847.3 0 52 78 50 847.3 0 50 79 52 847.3 0 52 80 53 847.3 0 53 81 41 847.3 0 41 82 57 847.3 0 57 83 62 847.3 0 62 84 46 847.3 0 46 85 55 847.3 0 55 86 54 847.3 0 54 87 63 847.3 0 63 88 90 847.3 0 90 89 49 847.3 0 49 90 68 847.3 0 68 91 57 847.3 0 57 92 53 847.3 0 53 93 60 847.3 0 60 94 44 847.3 0 44 95 42 847.3 0 42 96 32 847.3 0 32 97 53 847.3 0 53 98 88 847.3 0 88 99 41 847.3 0 41 100 34 847.3 0 34 101 45 847.3 0 45 102 30 847.3 0 30 103 28 847.3 0 28 104 41 847.3 0 41 105 40 847.3 0 40 106 71 847.3 0 71 107 53 847.3 0 53 108 42 847.3 0 42 109 46 847.3 0 46 110 63 847.3 0 63 111 49 847.3 0 49 112 57 847.3 0 57 113 39 847.3 0 39 114 52 847.3 0 52 115 40 847.3 0 40 116 44 847.3 0 44 117 139 847.3 0 139 118 190 847.3 0 190 119 519 847.3 0 519 120 44 847.3 0 44 121 49 847.3 0 49 122 43 847.3 0 43 123 57 847.3 0 57 124 59 847.3 0 59 125 87 847.3 0 87 126 60 847.3 0 60 127 52 847.3 0 52 128 51 847.3 0 51 129 72 847.3 0 72 130 49 847.3 0 49 131 42 847.3 0 42 132 54 847.3 0 54 133 47 847.3 0 47 134 61 847.3 0 61 135 59 847.3 0 59 136 41 847.3 0 41 137 54 847.3 0 54 138 63 847.3 0 63 139 56 847.3 0 56 140 101 847.3 0 101 141 69 847.3 0 69 142 118 847.3 0 118 143 58 847.3 0 58 144 82 847.3 0 82 145 77 847.3 0 77 146 82 847.3 0 82 147 56 847.3 0 56 148 57 847.3 0 57 149 88 847.3 0 88 150 116 847.3 0 116 151 85 847.3 0 85 152 89 847.3 0 89 153 92 847.3 0 92 154 59 847.3 0 59 155 87 847.3 0 87 156 74 847.3 0 74 157 73 847.3 0 73 158 116 847.3 0 116 159 87 847.3 0 87 160 65 847.3 0 65 161 66 847.3 0 66 162 52 847.3 0 52 163 50 847.3 0 50 164 54 847.3 0 54 165 72 847.3 0 72 166 67 847.3 0 67 167 77 847.3 0 77 168 68 847.3 0 68 169 91 847.3 0 91 170 106 847.3 0 106 171 100 847.3 0 100 172 76 847.3 0 76 173 105 847.3 0 105 174 82 847.3 0 82 175 100 847.3 0 100 176 124 847.3 0 124 177 168 847.3 0 168 178 190 847.3 0 190 179 312 847.3 0 312 180 527 847.3 0 527 181 204 847.3 0 204 182 393 847.3 0 393 183 966 847.3 0 966 184 620 847.3 0 620 185 170 847.3 0 170 186 239 847.3 0 239 187 194 847.3 0 194 188 541 847.3 0 541 189 353 847.3 0 353 190 365 847.3 0 365 191 288 847.3 0 288 192 346 847.3 0 346 193 2754 847.3 0 2754 194 3879 847.3 0 3879 195 23015 847.3 0 23015 196 688 847.3 0 688 197 261 847.3 0 261 198 53 847.3 0 53 199 53 847.3 0 53 200 79 847.3 0 79 201 64 847.3 0 64 202 71 847.3 0 71 203 47 847.3 0 47 204 54 847.3 0 54 205 60 847.3 0 60 206 64 847.3 0 64 207 73 847.3 0 73 208 92 847.3 0 92 209 63 847.3 0 63 210 45 847.3 0 45 211 79 847.3 0 79 212 50 847.3 0 50 213 184 847.3 0 184 214 492 847.3 0 492 215 322 847.3 0 322 216 167 847.3 0 167 217 124 847.3 0 124 218 122 847.3 0 122 219 452 847.3 0 452 220 298 847.3 0 298 221 231 847.3 0 231 222 153 847.3 0 153 223 75 847.3 0 75 224 79 847.3 0 79 225 92 847.3 0 92 226 79 847.3 0 79 227 72 847.3 0 72 228 75 847.3 0 75 229 53 847.3 0 53 230 95 847.3 0 95 231 101 847.3 0 101 232 111 847.3 0 111 233 83 847.3 0 83 234 107 847.3 0 107 235 89 847.3 0 89 236 115 847.3 0 115 237 183 847.3 0 183 238 101 847.3 0 101 239 457 847.3 0 457 240 696 847.3 0 696 241 314 847.3 0 314 242 124 847.3 0 124 243 67 847.3 0 67 244 73 847.3 0 73 245 70 847.3 0 70 246 81 847.3 0 81 247 72 847.3 0 72 248 81 847.3 0 81 249 136 847.3 0 136 250 858 847.3 0 858 251 822 847.3 0 822 252 658 847.3 0 658 253 344 847.3 0 344 254 56 847.3 0 56 255 68 847.3 0 68 256 82 847.3 0 82 257 147 847.3 0 147 258 104 847.3 0 104 259 224 847.3 0 224 260 186 847.3 0 186 261 110 847.3 0 110 262 98 847.3 0 98 263 551 847.3 0 551 264 380 847.3 0 380 265 255 847.3 0 255 266 187 847.3 0 187 267 123 847.3 0 123 268 128 847.3 0 128 269 103 847.3 0 103 270 87 847.3 0 87 271 72 847.3 0 72 272 77 847.3 0 77 273 71 847.3 0 71 274 82 847.3 0 82 275 95 847.3 0 95 276 89 847.3 0 89 277 79 847.3 0 79 278 88 847.3 0 88 279 84 847.3 0 84 280 82 847.3 0 82 281 79 847.3 0 79 282 96 847.3 0 96 283 116 847.3 0 116 284 103 847.3 0 103 285 89 847.3 0 89 286 123 847.3 0 123 287 175 847.3 0 175 288 2194 847.3 0 2194 289 1888 847.3 0 1888 290 1087 847.3 0 1087 291 159 847.3 0 159 292 58 847.3 0 58 293 86 847.3 0 86 294 97 847.3 0 97 295 81 847.3 0 81 296 95 847.3 0 95 297 118 847.3 0 118 298 120 847.3 0 120 299 110 847.3 0 110 300 139 847.3 0 139 301 141 847.3 0 141 Finished in 36.23 s (70 us/read; 0.86 M reads/minute). === Summary === Total reads processed: 520,490 Reads with adapters: 9,620 (1.8%) Reads that were too short: 121 (0.0%) Reads written (passing filters): 9,499 (1.8%) Total basepairs processed: 128,627,688 bp Total written (filtered): 2,106,579 bp (1.6%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 9620 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 3 0.0 3 0 0 3 19 86 0.0 3 0 84 2 20 4800 0.0 4 4725 73 2 21 10 0.0 4 3 7 22 6 0.0 4 5 0 1 23 4 0.0 4 0 0 0 4 40 1 0.0 4 0 0 0 1 42 1 0.0 4 1 46 1 0.0 4 1 47 1 0.0 4 1 50 2 0.0 4 0 0 0 0 2 69 1 0.0 4 0 1 72 2 0.0 4 0 0 0 0 2 76 1 0.0 4 0 0 0 0 1 77 1 0.0 4 0 0 0 0 1 78 1 0.0 4 0 0 0 0 1 81 2 0.0 4 1 0 0 0 1 82 2 0.0 4 0 0 0 0 2 83 4 0.0 4 0 0 0 0 4 84 4 0.0 4 0 0 0 0 4 85 3785 0.0 4 0 0 0 0 3785 88 1 0.0 4 0 0 0 0 1 98 2 0.0 4 0 0 0 0 2 99 1 0.0 4 0 0 1 110 2 0.0 4 0 0 0 0 2 111 5 0.0 4 0 0 0 0 5 112 1 0.0 4 0 0 0 0 1 113 1 0.0 4 0 0 0 0 1 114 759 0.0 4 0 0 0 0 759 115 2 0.0 4 0 0 0 0 2 126 1 0.0 4 0 0 0 0 1 127 3 0.0 4 0 0 0 0 3 140 2 0.0 4 0 0 0 0 2 141 1 0.0 4 0 0 0 0 1 151 1 0.0 4 0 0 0 0 1 160 1 0.0 4 0 0 0 0 1 162 1 0.0 4 0 1 164 1 0.0 4 0 0 0 0 1 171 1 0.0 4 0 0 0 0 1 172 1 0.0 4 0 0 0 0 1 173 3 0.0 4 0 0 0 0 3 174 1 0.0 4 0 0 0 0 1 184 1 0.0 4 0 0 0 0 1 185 1 0.0 4 0 0 0 0 1 186 10 0.0 4 0 0 0 0 10 187 2 0.0 4 0 0 0 0 2 188 1 0.0 4 0 0 0 0 1 191 1 0.0 4 0 0 0 0 1 192 1 0.0 4 0 0 0 0 1 201 1 0.0 4 0 0 0 0 1 207 2 0.0 4 0 0 0 0 2 215 9 0.0 4 0 0 0 0 9 216 3 0.0 4 0 0 0 0 3 217 1 0.0 4 0 0 0 0 1 218 12 0.0 4 0 0 0 0 12 220 1 0.0 4 0 0 0 0 1 221 5 0.0 4 0 0 0 0 5 222 11 0.0 4 0 0 0 1 10 223 8 0.0 4 0 0 0 0 8 226 1 0.0 4 0 0 0 0 1 227 1 0.0 4 0 0 0 0 1 228 1 0.0 4 0 0 0 0 1 235 1 0.0 4 0 0 0 0 1 237 1 0.0 4 0 0 0 0 1 239 1 0.0 4 0 0 0 0 1 240 2 0.0 4 0 0 0 0 2 242 1 0.0 4 0 0 0 0 1 243 1 0.0 4 0 0 0 0 1 246 4 0.0 4 0 0 0 0 4 249 2 0.0 4 0 0 0 0 2 250 2 0.0 4 0 0 0 0 2 251 5 0.0 4 0 0 0 0 5 252 6 0.0 4 0 0 0 0 6 253 2 0.0 4 0 0 0 0 2 256 1 0.0 4 0 0 0 0 1 257 1 0.0 4 0 0 0 0 1 262 2 0.0 4 0 0 0 1 1 263 1 0.0 4 0 0 0 0 1 270 1 0.0 4 0 1 276 1 0.0 4 0 0 0 1 278 1 0.0 4 0 0 0 0 1 280 1 0.0 4 0 0 0 0 1 282 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 0.49 s (52 us/read; 1.16 M reads/minute). === Summary === Total reads processed: 9,499 Reads with adapters: 319 (3.4%) Reads written (passing filters): 9,499 (100.0%) Total basepairs processed: 2,106,579 bp Total written (filtered): 2,102,430 bp (99.8%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 319 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 11.9% C: 2.2% G: 83.4% T: 2.5% 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 15 148.4 0 15 4 23 37.1 0 23 5 2 9.3 0 2 9 1 0.0 0 0 1 10 47 0.0 1 3 44 11 225 0.0 1 16 209 13 1 0.0 1 1 139 1 0.0 1 1 224 4 0.0 1 4 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.