This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TTCGGA -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 173.47 s (50 us/read; 1.20 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 704,979 (20.3%) Reads that were too short: 37,589 (1.1%) Reads written (passing filters): 667,390 (19.2%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 154,425,545 bp (14.8%) === Adapter 1 === Sequence: TTCGGA; Type: regular 5'; Length: 6; Trimmed: 704979 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1969 847.3 0 1969 7 4389 847.3 0 4389 8 111405 847.3 0 111405 9 90086 847.3 0 90086 10 202 847.3 0 202 11 36 847.3 0 36 12 35 847.3 0 35 13 24 847.3 0 24 14 24 847.3 0 24 15 24 847.3 0 24 16 37 847.3 0 37 17 43 847.3 0 43 18 25 847.3 0 25 19 36 847.3 0 36 20 33 847.3 0 33 21 37 847.3 0 37 22 53 847.3 0 53 23 77 847.3 0 77 24 71 847.3 0 71 25 39 847.3 0 39 26 75 847.3 0 75 27 66 847.3 0 66 28 29 847.3 0 29 29 32 847.3 0 32 30 35 847.3 0 35 31 50 847.3 0 50 32 70 847.3 0 70 33 28 847.3 0 28 34 28 847.3 0 28 35 38 847.3 0 38 36 24 847.3 0 24 37 39 847.3 0 39 38 118 847.3 0 118 39 136 847.3 0 136 40 145 847.3 0 145 41 246 847.3 0 246 42 81 847.3 0 81 43 33 847.3 0 33 44 22 847.3 0 22 45 21 847.3 0 21 46 35 847.3 0 35 47 38 847.3 0 38 48 58 847.3 0 58 49 73 847.3 0 73 50 79 847.3 0 79 51 60 847.3 0 60 52 87 847.3 0 87 53 118 847.3 0 118 54 139 847.3 0 139 55 35 847.3 0 35 56 43 847.3 0 43 57 105 847.3 0 105 58 87 847.3 0 87 59 59 847.3 0 59 60 113 847.3 0 113 61 57 847.3 0 57 62 116 847.3 0 116 63 113 847.3 0 113 64 41 847.3 0 41 65 80 847.3 0 80 66 151 847.3 0 151 67 111 847.3 0 111 68 334 847.3 0 334 69 127 847.3 0 127 70 109 847.3 0 109 71 83 847.3 0 83 72 281 847.3 0 281 73 190 847.3 0 190 74 280 847.3 0 280 75 456 847.3 0 456 76 676 847.3 0 676 77 858 847.3 0 858 78 1768 847.3 0 1768 79 3382 847.3 0 3382 80 844 847.3 0 844 81 1223 847.3 0 1223 82 2154 847.3 0 2154 83 1220 847.3 0 1220 84 1030 847.3 0 1030 85 2513 847.3 0 2513 86 2069 847.3 0 2069 87 2101 847.3 0 2101 88 2216 847.3 0 2216 89 3281 847.3 0 3281 90 5414 847.3 0 5414 91 9195 847.3 0 9195 92 192608 847.3 0 192608 93 111411 847.3 0 111411 94 82109 847.3 0 82109 95 790 847.3 0 790 96 36 847.3 0 36 97 63 847.3 0 63 98 107 847.3 0 107 99 46 847.3 0 46 100 37 847.3 0 37 101 18 847.3 0 18 102 21 847.3 0 21 103 21 847.3 0 21 104 20 847.3 0 20 105 16 847.3 0 16 106 20 847.3 0 20 107 34 847.3 0 34 108 32 847.3 0 32 109 61 847.3 0 61 110 150 847.3 0 150 111 86 847.3 0 86 112 57 847.3 0 57 113 24 847.3 0 24 114 56 847.3 0 56 115 38 847.3 0 38 116 47 847.3 0 47 117 35 847.3 0 35 118 50 847.3 0 50 119 222 847.3 0 222 120 21 847.3 0 21 121 17 847.3 0 17 122 19 847.3 0 19 123 10 847.3 0 10 124 12 847.3 0 12 125 34 847.3 0 34 126 21 847.3 0 21 127 17 847.3 0 17 128 50 847.3 0 50 129 132 847.3 0 132 130 40 847.3 0 40 131 54 847.3 0 54 132 24 847.3 0 24 133 54 847.3 0 54 134 312 847.3 0 312 135 26 847.3 0 26 136 33 847.3 0 33 137 44 847.3 0 44 138 53 847.3 0 53 139 30 847.3 0 30 140 25 847.3 0 25 141 18 847.3 0 18 142 25 847.3 0 25 143 44 847.3 0 44 144 45 847.3 0 45 145 33 847.3 0 33 146 19 847.3 0 19 147 12 847.3 0 12 148 24 847.3 0 24 149 22 847.3 0 22 150 22 847.3 0 22 151 28 847.3 0 28 152 26 847.3 0 26 153 21 847.3 0 21 154 30 847.3 0 30 155 27 847.3 0 27 156 25 847.3 0 25 157 34 847.3 0 34 158 37 847.3 0 37 159 33 847.3 0 33 160 36 847.3 0 36 161 28 847.3 0 28 162 23 847.3 0 23 163 25 847.3 0 25 164 26 847.3 0 26 165 34 847.3 0 34 166 27 847.3 0 27 167 24 847.3 0 24 168 19 847.3 0 19 169 30 847.3 0 30 170 18 847.3 0 18 171 36 847.3 0 36 172 33 847.3 0 33 173 33 847.3 0 33 174 44 847.3 0 44 175 31 847.3 0 31 176 42 847.3 0 42 177 78 847.3 0 78 178 302 847.3 0 302 179 728 847.3 0 728 180 765 847.3 0 765 181 170 847.3 0 170 182 35 847.3 0 35 183 48 847.3 0 48 184 66 847.3 0 66 185 77 847.3 0 77 186 116 847.3 0 116 187 191 847.3 0 191 188 348 847.3 0 348 189 111 847.3 0 111 190 203 847.3 0 203 191 213 847.3 0 213 192 204 847.3 0 204 193 123 847.3 0 123 194 205 847.3 0 205 195 211 847.3 0 211 196 272 847.3 0 272 197 281 847.3 0 281 198 367 847.3 0 367 199 480 847.3 0 480 200 954 847.3 0 954 201 17002 847.3 0 17002 202 12412 847.3 0 12412 203 4945 847.3 0 4945 204 372 847.3 0 372 205 1287 847.3 0 1287 206 1381 847.3 0 1381 207 1269 847.3 0 1269 208 651 847.3 0 651 209 427 847.3 0 427 210 162 847.3 0 162 211 61 847.3 0 61 212 70 847.3 0 70 213 76 847.3 0 76 214 41 847.3 0 41 215 84 847.3 0 84 216 122 847.3 0 122 217 195 847.3 0 195 218 80 847.3 0 80 219 201 847.3 0 201 220 85 847.3 0 85 221 273 847.3 0 273 222 154 847.3 0 154 223 205 847.3 0 205 224 152 847.3 0 152 225 288 847.3 0 288 226 984 847.3 0 984 227 964 847.3 0 964 228 751 847.3 0 751 229 123 847.3 0 123 230 40 847.3 0 40 231 42 847.3 0 42 232 48 847.3 0 48 233 37 847.3 0 37 234 29 847.3 0 29 235 29 847.3 0 29 236 93 847.3 0 93 237 65 847.3 0 65 238 58 847.3 0 58 239 24 847.3 0 24 240 16 847.3 0 16 241 14 847.3 0 14 242 23 847.3 0 23 243 36 847.3 0 36 244 36 847.3 0 36 245 43 847.3 0 43 246 50 847.3 0 50 247 36 847.3 0 36 248 46 847.3 0 46 249 49 847.3 0 49 250 34 847.3 0 34 251 29 847.3 0 29 252 29 847.3 0 29 253 36 847.3 0 36 254 51 847.3 0 51 255 53 847.3 0 53 256 60 847.3 0 60 257 66 847.3 0 66 258 74 847.3 0 74 259 267 847.3 0 267 260 633 847.3 0 633 261 1043 847.3 0 1043 262 733 847.3 0 733 263 419 847.3 0 419 264 265 847.3 0 265 265 67 847.3 0 67 266 40 847.3 0 40 267 33 847.3 0 33 268 28 847.3 0 28 269 50 847.3 0 50 270 196 847.3 0 196 271 225 847.3 0 225 272 139 847.3 0 139 273 116 847.3 0 116 274 29 847.3 0 29 275 52 847.3 0 52 276 39 847.3 0 39 277 92 847.3 0 92 278 69 847.3 0 69 279 62 847.3 0 62 280 81 847.3 0 81 281 137 847.3 0 137 282 132 847.3 0 132 283 90 847.3 0 90 284 100 847.3 0 100 285 535 847.3 0 535 286 392 847.3 0 392 287 357 847.3 0 357 288 85 847.3 0 85 289 24 847.3 0 24 290 38 847.3 0 38 291 38 847.3 0 38 292 24 847.3 0 24 293 28 847.3 0 28 294 53 847.3 0 53 295 96 847.3 0 96 296 148 847.3 0 148 297 989 847.3 0 989 298 289 847.3 0 289 299 223 847.3 0 223 300 45 847.3 0 45 301 27 847.3 0 27 Finished in 45.64 s (68 us/read; 0.88 M reads/minute). === Summary === Total reads processed: 667,390 Reads with adapters: 97,636 (14.6%) Reads that were too short: 175 (0.0%) Reads written (passing filters): 97,461 (14.6%) Total basepairs processed: 154,425,545 bp Total written (filtered): 26,348,740 bp (17.1%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 97636 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 7 0.0 3 0 0 0 3 4 18 58 0.0 3 0 0 43 9 6 19 1927 0.0 3 0 1777 94 36 20 20 93338 0.0 4 88816 3698 603 180 41 21 226 0.0 4 33 174 9 7 3 22 27 0.0 4 1 0 14 3 9 23 291 0.0 4 1 0 0 215 75 24 3 0.0 4 1 0 0 0 2 25 1 0.0 4 1 26 1 0.0 4 0 1 29 1 0.0 4 0 0 0 0 1 31 1 0.0 4 1 38 2 0.0 4 0 0 0 0 2 40 1 0.0 4 1 43 4 0.0 4 0 0 0 0 4 51 1 0.0 4 0 0 0 0 1 52 1 0.0 4 0 1 53 1 0.0 4 0 0 0 0 1 63 3 0.0 4 0 0 0 0 3 64 1 0.0 4 1 67 4 0.0 4 0 0 0 0 4 68 57 0.0 4 0 0 0 0 57 88 1 0.0 4 1 91 2 0.0 4 0 0 0 0 2 94 11 0.0 4 0 0 0 0 11 96 2 0.0 4 0 0 0 0 2 121 1 0.0 4 0 0 0 0 1 122 5 0.0 4 0 0 0 0 5 123 7 0.0 4 0 0 0 2 5 124 1 0.0 4 0 0 0 0 1 125 3 0.0 4 0 0 0 0 3 126 13 0.0 4 0 0 0 0 13 127 1475 0.0 4 0 0 0 0 1475 128 6 0.0 4 0 0 0 0 6 130 4 0.0 4 0 0 0 0 4 131 2 0.0 4 0 0 0 0 2 135 1 0.0 4 0 0 0 0 1 136 1 0.0 4 0 0 0 0 1 137 4 0.0 4 0 0 0 0 4 138 2 0.0 4 0 0 0 0 2 140 7 0.0 4 0 0 0 1 6 141 1 0.0 4 0 0 0 0 1 142 1 0.0 4 0 0 0 0 1 148 3 0.0 4 0 0 0 0 3 149 15 0.0 4 0 0 0 0 15 150 11 0.0 4 0 0 0 0 11 151 14 0.0 4 0 0 0 0 14 152 1 0.0 4 0 0 0 0 1 153 7 0.0 4 0 0 0 0 7 155 1 0.0 4 0 0 0 0 1 158 1 0.0 4 0 0 0 0 1 166 1 0.0 4 0 0 0 0 1 171 2 0.0 4 0 0 0 0 2 172 2 0.0 4 0 0 0 0 2 173 4 0.0 4 0 0 0 0 4 174 3 0.0 4 0 0 0 0 3 176 1 0.0 4 0 0 0 0 1 177 1 0.0 4 0 0 0 0 1 185 1 0.0 4 0 0 0 0 1 194 1 0.0 4 0 0 0 0 1 197 1 0.0 4 0 0 0 0 1 198 2 0.0 4 0 0 0 0 2 203 1 0.0 4 0 0 0 0 1 204 1 0.0 4 0 0 0 0 1 206 2 0.0 4 0 0 0 0 2 207 1 0.0 4 0 0 0 0 1 208 1 0.0 4 0 0 0 0 1 209 1 0.0 4 0 0 0 0 1 213 1 0.0 4 0 0 0 0 1 214 2 0.0 4 0 0 0 0 2 215 1 0.0 4 0 0 0 0 1 216 3 0.0 4 0 0 0 0 3 217 2 0.0 4 0 0 0 0 2 220 1 0.0 4 0 0 0 0 1 228 5 0.0 4 0 0 0 0 5 229 3 0.0 4 0 0 0 0 3 230 1 0.0 4 0 0 0 0 1 233 2 0.0 4 0 0 0 0 2 235 5 0.0 4 0 0 0 0 5 236 1 0.0 4 0 0 0 0 1 237 1 0.0 4 0 0 0 0 1 257 1 0.0 4 0 0 0 0 1 262 1 0.0 4 0 0 0 0 1 263 4 0.0 4 0 0 0 0 4 264 6 0.0 4 0 0 0 0 6 265 4 0.0 4 0 0 0 0 4 282 2 0.0 4 0 0 0 0 2 285 1 0.0 4 0 0 0 0 1 286 1 0.0 4 0 0 0 0 1 292 1 0.0 4 0 0 0 0 1 293 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 6.05 s (62 us/read; 0.97 M reads/minute). === Summary === Total reads processed: 97,461 Reads with adapters: 28,065 (28.8%) Reads written (passing filters): 97,461 (100.0%) Total basepairs processed: 26,348,740 bp Total written (filtered): 26,065,231 bp (98.9%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 28065 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.5% C: 5.2% G: 91.9% T: 1.5% 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 50 1522.8 0 50 4 39 380.7 0 39 5 1 95.2 0 1 6 4 23.8 0 4 7 9 5.9 0 9 8 7 1.5 0 7 9 15604 0.4 0 1110 14494 10 9131 0.1 1 585 8546 11 3031 0.0 1 67 2964 12 70 0.0 1 2 68 13 24 0.0 1 0 24 14 4 0.0 1 0 4 15 1 0.0 1 0 1 17 1 0.0 1 0 1 24 1 0.0 1 1 121 1 0.0 1 0 1 138 1 0.0 1 1 150 19 0.0 1 10 9 151 1 0.0 1 1 152 2 0.0 1 1 1 169 2 0.0 1 1 1 189 5 0.0 1 0 5 191 1 0.0 1 0 1 192 1 0.0 1 0 1 208 50 0.0 1 42 8 209 1 0.0 1 1 210 2 0.0 1 2 222 1 0.0 1 0 1 223 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.