This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g GCGAGA -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 163.45 s (47 us/read; 1.27 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 137,217 (4.0%) Reads that were too short: 23,292 (0.7%) Reads written (passing filters): 113,925 (3.3%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 30,339,076 bp (2.9%) === Adapter 1 === Sequence: GCGAGA; Type: regular 5'; Length: 6; Trimmed: 137217 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 6022 847.3 0 6022 7 36782 847.3 0 36782 8 43305 847.3 0 43305 9 92 847.3 0 92 10 49 847.3 0 49 11 54 847.3 0 54 12 51 847.3 0 51 13 52 847.3 0 52 14 56 847.3 0 56 15 50 847.3 0 50 16 23 847.3 0 23 17 30 847.3 0 30 18 27 847.3 0 27 19 31 847.3 0 31 20 40 847.3 0 40 21 38 847.3 0 38 22 47 847.3 0 47 23 51 847.3 0 51 24 41 847.3 0 41 25 39 847.3 0 39 26 43 847.3 0 43 27 38 847.3 0 38 28 43 847.3 0 43 29 44 847.3 0 44 30 51 847.3 0 51 31 76 847.3 0 76 32 48 847.3 0 48 33 57 847.3 0 57 34 48 847.3 0 48 35 45 847.3 0 45 36 62 847.3 0 62 37 81 847.3 0 81 38 34 847.3 0 34 39 64 847.3 0 64 40 77 847.3 0 77 41 54 847.3 0 54 42 40 847.3 0 40 43 83 847.3 0 83 44 66 847.3 0 66 45 62 847.3 0 62 46 63 847.3 0 63 47 78 847.3 0 78 48 109 847.3 0 109 49 96 847.3 0 96 50 1845 847.3 0 1845 51 2882 847.3 0 2882 52 888 847.3 0 888 53 34 847.3 0 34 54 40 847.3 0 40 55 24 847.3 0 24 56 23 847.3 0 23 57 43 847.3 0 43 58 36 847.3 0 36 59 35 847.3 0 35 60 56 847.3 0 56 61 66 847.3 0 66 62 30 847.3 0 30 63 97 847.3 0 97 64 50 847.3 0 50 65 68 847.3 0 68 66 54 847.3 0 54 67 43 847.3 0 43 68 44 847.3 0 44 69 41 847.3 0 41 70 43 847.3 0 43 71 44 847.3 0 44 72 60 847.3 0 60 73 73 847.3 0 73 74 342 847.3 0 342 75 305 847.3 0 305 76 371 847.3 0 371 77 48 847.3 0 48 78 102 847.3 0 102 79 50 847.3 0 50 80 56 847.3 0 56 81 56 847.3 0 56 82 54 847.3 0 54 83 42 847.3 0 42 84 35 847.3 0 35 85 46 847.3 0 46 86 35 847.3 0 35 87 40 847.3 0 40 88 36 847.3 0 36 89 44 847.3 0 44 90 61 847.3 0 61 91 43 847.3 0 43 92 38 847.3 0 38 93 46 847.3 0 46 94 33 847.3 0 33 95 38 847.3 0 38 96 45 847.3 0 45 97 33 847.3 0 33 98 66 847.3 0 66 99 61 847.3 0 61 100 49 847.3 0 49 101 68 847.3 0 68 102 71 847.3 0 71 103 56 847.3 0 56 104 68 847.3 0 68 105 45 847.3 0 45 106 46 847.3 0 46 107 58 847.3 0 58 108 37 847.3 0 37 109 53 847.3 0 53 110 51 847.3 0 51 111 57 847.3 0 57 112 77 847.3 0 77 113 58 847.3 0 58 114 88 847.3 0 88 115 104 847.3 0 104 116 77 847.3 0 77 117 120 847.3 0 120 118 81 847.3 0 81 119 92 847.3 0 92 120 80 847.3 0 80 121 83 847.3 0 83 122 90 847.3 0 90 123 74 847.3 0 74 124 120 847.3 0 120 125 1463 847.3 0 1463 126 1641 847.3 0 1641 127 412 847.3 0 412 128 72 847.3 0 72 129 82 847.3 0 82 130 237 847.3 0 237 131 164 847.3 0 164 132 170 847.3 0 170 133 48 847.3 0 48 134 40 847.3 0 40 135 70 847.3 0 70 136 191 847.3 0 191 137 73 847.3 0 73 138 61 847.3 0 61 139 50 847.3 0 50 140 42 847.3 0 42 141 39 847.3 0 39 142 50 847.3 0 50 143 40 847.3 0 40 144 63 847.3 0 63 145 60 847.3 0 60 146 42 847.3 0 42 147 50 847.3 0 50 148 46 847.3 0 46 149 38 847.3 0 38 150 45 847.3 0 45 151 66 847.3 0 66 152 49 847.3 0 49 153 56 847.3 0 56 154 42 847.3 0 42 155 34 847.3 0 34 156 42 847.3 0 42 157 71 847.3 0 71 158 38 847.3 0 38 159 47 847.3 0 47 160 48 847.3 0 48 161 46 847.3 0 46 162 53 847.3 0 53 163 54 847.3 0 54 164 359 847.3 0 359 165 288 847.3 0 288 166 317 847.3 0 317 167 57 847.3 0 57 168 86 847.3 0 86 169 42 847.3 0 42 170 69 847.3 0 69 171 55 847.3 0 55 172 52 847.3 0 52 173 60 847.3 0 60 174 68 847.3 0 68 175 43 847.3 0 43 176 58 847.3 0 58 177 79 847.3 0 79 178 68 847.3 0 68 179 82 847.3 0 82 180 53 847.3 0 53 181 87 847.3 0 87 182 70 847.3 0 70 183 97 847.3 0 97 184 80 847.3 0 80 185 69 847.3 0 69 186 79 847.3 0 79 187 95 847.3 0 95 188 63 847.3 0 63 189 96 847.3 0 96 190 89 847.3 0 89 191 337 847.3 0 337 192 283 847.3 0 283 193 152 847.3 0 152 194 161 847.3 0 161 195 157 847.3 0 157 196 1129 847.3 0 1129 197 1547 847.3 0 1547 198 1509 847.3 0 1509 199 723 847.3 0 723 200 314 847.3 0 314 201 127 847.3 0 127 202 167 847.3 0 167 203 172 847.3 0 172 204 1729 847.3 0 1729 205 995 847.3 0 995 206 2812 847.3 0 2812 207 113 847.3 0 113 208 115 847.3 0 115 209 103 847.3 0 103 210 105 847.3 0 105 211 111 847.3 0 111 212 78 847.3 0 78 213 92 847.3 0 92 214 89 847.3 0 89 215 100 847.3 0 100 216 763 847.3 0 763 217 774 847.3 0 774 218 417 847.3 0 417 219 166 847.3 0 166 220 108 847.3 0 108 221 84 847.3 0 84 222 86 847.3 0 86 223 92 847.3 0 92 224 79 847.3 0 79 225 92 847.3 0 92 226 108 847.3 0 108 227 66 847.3 0 66 228 90 847.3 0 90 229 66 847.3 0 66 230 79 847.3 0 79 231 56 847.3 0 56 232 55 847.3 0 55 233 51 847.3 0 51 234 91 847.3 0 91 235 148 847.3 0 148 236 51 847.3 0 51 237 79 847.3 0 79 238 85 847.3 0 85 239 138 847.3 0 138 240 124 847.3 0 124 241 198 847.3 0 198 242 89 847.3 0 89 243 80 847.3 0 80 244 67 847.3 0 67 245 70 847.3 0 70 246 100 847.3 0 100 247 640 847.3 0 640 248 1029 847.3 0 1029 249 945 847.3 0 945 250 606 847.3 0 606 251 135 847.3 0 135 252 91 847.3 0 91 253 77 847.3 0 77 254 83 847.3 0 83 255 75 847.3 0 75 256 71 847.3 0 71 257 89 847.3 0 89 258 76 847.3 0 76 259 95 847.3 0 95 260 226 847.3 0 226 261 80 847.3 0 80 262 140 847.3 0 140 263 83 847.3 0 83 264 79 847.3 0 79 265 73 847.3 0 73 266 70 847.3 0 70 267 63 847.3 0 63 268 58 847.3 0 58 269 473 847.3 0 473 270 404 847.3 0 404 271 607 847.3 0 607 272 67 847.3 0 67 273 74 847.3 0 74 274 71 847.3 0 71 275 73 847.3 0 73 276 70 847.3 0 70 277 82 847.3 0 82 278 93 847.3 0 93 279 155 847.3 0 155 280 120 847.3 0 120 281 79 847.3 0 79 282 74 847.3 0 74 283 66 847.3 0 66 284 65 847.3 0 65 285 81 847.3 0 81 286 123 847.3 0 123 287 94 847.3 0 94 288 84 847.3 0 84 289 410 847.3 0 410 290 854 847.3 0 854 291 1059 847.3 0 1059 292 480 847.3 0 480 293 210 847.3 0 210 294 93 847.3 0 93 295 62 847.3 0 62 296 85 847.3 0 85 297 167 847.3 0 167 298 158 847.3 0 158 299 251 847.3 0 251 300 170 847.3 0 170 301 121 847.3 0 121 Finished in 8.76 s (77 us/read; 0.78 M reads/minute). === Summary === Total reads processed: 113,925 Reads with adapters: 48,917 (42.9%) Reads that were too short: 34 (0.0%) Reads written (passing filters): 48,883 (42.9%) Total basepairs processed: 30,339,076 bp Total written (filtered): 13,290,117 bp (43.8%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 48917 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 16 1 0.0 3 0 0 0 0 1 17 7 0.0 3 0 0 0 2 5 18 24 0.0 3 0 0 24 19 560 0.0 3 0 547 7 5 1 20 43623 0.0 4 42934 657 19 3 10 21 171 0.0 4 60 106 2 3 22 54 0.0 4 10 32 7 5 23 3934 0.0 4 3828 70 1 31 4 24 12 0.0 4 3 7 0 0 2 25 4 0.0 4 1 1 1 0 1 26 1 0.0 4 0 0 0 0 1 33 1 0.0 4 1 34 1 0.0 4 1 36 1 0.0 4 1 45 1 0.0 4 0 0 0 0 1 46 1 0.0 4 0 0 0 0 1 60 1 0.0 4 0 0 0 0 1 73 2 0.0 4 0 0 0 0 2 75 1 0.0 4 0 0 0 0 1 84 5 0.0 4 0 0 0 0 5 92 1 0.0 4 0 0 0 0 1 111 1 0.0 4 0 0 0 0 1 121 1 0.0 4 1 125 1 0.0 4 0 0 0 0 1 126 9 0.0 4 0 0 0 0 9 127 461 0.0 4 0 0 0 0 461 128 2 0.0 4 0 0 0 0 2 132 1 0.0 4 1 139 1 0.0 4 1 140 1 0.0 4 0 0 0 1 144 1 0.0 4 0 0 0 0 1 153 2 0.0 4 0 0 0 0 2 154 2 0.0 4 0 0 0 0 2 175 1 0.0 4 0 0 0 0 1 185 5 0.0 4 0 0 0 0 5 186 3 0.0 4 0 0 0 0 3 193 1 0.0 4 0 0 0 0 1 194 1 0.0 4 1 202 1 0.0 4 0 0 0 0 1 205 1 0.0 4 0 0 0 0 1 214 2 0.0 4 0 0 0 0 2 228 2 0.0 4 0 0 0 0 2 233 1 0.0 4 0 0 0 0 1 234 1 0.0 4 0 0 0 0 1 235 1 0.0 4 0 0 0 0 1 244 1 0.0 4 0 0 0 0 1 260 1 0.0 4 0 0 0 0 1 264 1 0.0 4 0 0 0 0 1 282 2 0.0 4 0 0 0 0 2 283 1 0.0 4 0 0 0 0 1 288 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 2.83 s (58 us/read; 1.04 M reads/minute). === Summary === Total reads processed: 48,883 Reads with adapters: 4,179 (8.5%) Reads written (passing filters): 48,883 (100.0%) Total basepairs processed: 13,290,117 bp Total written (filtered): 13,237,694 bp (99.6%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 4179 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.4% C: 2.6% G: 94.0% T: 1.9% 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 21 763.8 0 21 4 67 190.9 0 67 5 5 47.7 0 5 7 1 3.0 0 1 9 811 0.2 0 17 794 10 1586 0.0 1 51 1535 11 1624 0.0 1 11 1613 12 2 0.0 1 0 2 13 2 0.0 1 0 2 151 27 0.0 1 24 3 159 1 0.0 1 0 1 208 1 0.0 1 0 1 209 24 0.0 1 19 5 210 2 0.0 1 2 211 1 0.0 1 0 1 224 4 0.0 1 4 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.