This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CGGCCA -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 90.47 s (26 us/read; 2.30 M reads/minute). === Summary === Total reads processed: 3,465,239 Reads with adapters: 75,426 (2.2%) Reads that were too short: 33,487 (1.0%) Reads written (passing filters): 41,939 (1.2%) Total basepairs processed: 1,043,036,939 bp Total written (filtered): 10,082,863 bp (1.0%) === Adapter 1 === Sequence: CGGCCA; Type: regular 5'; Length: 6; Trimmed: 75426 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 857 846.0 0 857 7 17089 846.0 0 17089 8 37 846.0 0 37 9 31 846.0 0 31 10 38 846.0 0 38 11 51 846.0 0 51 12 36 846.0 0 36 13 27 846.0 0 27 14 22 846.0 0 22 15 19 846.0 0 19 16 20 846.0 0 20 17 23 846.0 0 23 18 24 846.0 0 24 19 31 846.0 0 31 20 25 846.0 0 25 21 31 846.0 0 31 22 21 846.0 0 21 23 25 846.0 0 25 24 22 846.0 0 22 25 20 846.0 0 20 26 27 846.0 0 27 27 28 846.0 0 28 28 32 846.0 0 32 29 32 846.0 0 32 30 39 846.0 0 39 31 45 846.0 0 45 32 39 846.0 0 39 33 31 846.0 0 31 34 25 846.0 0 25 35 29 846.0 0 29 36 29 846.0 0 29 37 6919 846.0 0 6919 38 33 846.0 0 33 39 34 846.0 0 34 40 95 846.0 0 95 41 64 846.0 0 64 42 45 846.0 0 45 43 40 846.0 0 40 44 26 846.0 0 26 45 17 846.0 0 17 46 18 846.0 0 18 47 30 846.0 0 30 48 42 846.0 0 42 49 28 846.0 0 28 50 19 846.0 0 19 51 21 846.0 0 21 52 25 846.0 0 25 53 38 846.0 0 38 54 34 846.0 0 34 55 43 846.0 0 43 56 29 846.0 0 29 57 52 846.0 0 52 58 20 846.0 0 20 59 32 846.0 0 32 60 27 846.0 0 27 61 21 846.0 0 21 62 23 846.0 0 23 63 31 846.0 0 31 64 325 846.0 0 325 65 75 846.0 0 75 66 118 846.0 0 118 67 30 846.0 0 30 68 18 846.0 0 18 69 20 846.0 0 20 70 21 846.0 0 21 71 35 846.0 0 35 72 31 846.0 0 31 73 124 846.0 0 124 74 366 846.0 0 366 75 108 846.0 0 108 76 55 846.0 0 55 77 22 846.0 0 22 78 22 846.0 0 22 79 21 846.0 0 21 80 26 846.0 0 26 81 14 846.0 0 14 82 19 846.0 0 19 83 28 846.0 0 28 84 22 846.0 0 22 85 86 846.0 0 86 86 139 846.0 0 139 87 1487 846.0 0 1487 88 357 846.0 0 357 89 180 846.0 0 180 90 20 846.0 0 20 91 15 846.0 0 15 92 40 846.0 0 40 93 28 846.0 0 28 94 29 846.0 0 29 95 33 846.0 0 33 96 33 846.0 0 33 97 27 846.0 0 27 98 33 846.0 0 33 99 21 846.0 0 21 100 35 846.0 0 35 101 28 846.0 0 28 102 36 846.0 0 36 103 41 846.0 0 41 104 36 846.0 0 36 105 20 846.0 0 20 106 9 846.0 0 9 107 11 846.0 0 11 108 21 846.0 0 21 109 28 846.0 0 28 110 24 846.0 0 24 111 26 846.0 0 26 112 18 846.0 0 18 113 23 846.0 0 23 114 52 846.0 0 52 115 34 846.0 0 34 116 19 846.0 0 19 117 45 846.0 0 45 118 34 846.0 0 34 119 31 846.0 0 31 120 29 846.0 0 29 121 25 846.0 0 25 122 26 846.0 0 26 123 14 846.0 0 14 124 37 846.0 0 37 125 30 846.0 0 30 126 40 846.0 0 40 127 22 846.0 0 22 128 29 846.0 0 29 129 86 846.0 0 86 130 33 846.0 0 33 131 33 846.0 0 33 132 32 846.0 0 32 133 27 846.0 0 27 134 29 846.0 0 29 135 27 846.0 0 27 136 30 846.0 0 30 137 44 846.0 0 44 138 67 846.0 0 67 139 38 846.0 0 38 140 53 846.0 0 53 141 35 846.0 0 35 142 60 846.0 0 60 143 178 846.0 0 178 144 70 846.0 0 70 145 62 846.0 0 62 146 48 846.0 0 48 147 49 846.0 0 49 148 47 846.0 0 47 149 54 846.0 0 54 150 96 846.0 0 96 151 676 846.0 0 676 152 415 846.0 0 415 153 661 846.0 0 661 154 67 846.0 0 67 155 124 846.0 0 124 156 1472 846.0 0 1472 157 962 846.0 0 962 158 1695 846.0 0 1695 159 129 846.0 0 129 160 45 846.0 0 45 161 65 846.0 0 65 162 24 846.0 0 24 163 26 846.0 0 26 164 44 846.0 0 44 165 75 846.0 0 75 166 72 846.0 0 72 167 63 846.0 0 63 168 42 846.0 0 42 169 43 846.0 0 43 170 190 846.0 0 190 171 607 846.0 0 607 172 143 846.0 0 143 173 52 846.0 0 52 174 43 846.0 0 43 175 105 846.0 0 105 176 363 846.0 0 363 177 169 846.0 0 169 178 179 846.0 0 179 179 56 846.0 0 56 180 27 846.0 0 27 181 33 846.0 0 33 182 30 846.0 0 30 183 32 846.0 0 32 184 85 846.0 0 85 185 31 846.0 0 31 186 33 846.0 0 33 187 28 846.0 0 28 188 32 846.0 0 32 189 24 846.0 0 24 190 18 846.0 0 18 191 25 846.0 0 25 192 23 846.0 0 23 193 31 846.0 0 31 194 22 846.0 0 22 195 44 846.0 0 44 196 29 846.0 0 29 197 22 846.0 0 22 198 12 846.0 0 12 199 21 846.0 0 21 200 43 846.0 0 43 201 27 846.0 0 27 202 34 846.0 0 34 203 27 846.0 0 27 204 9 846.0 0 9 205 48 846.0 0 48 206 40 846.0 0 40 207 33 846.0 0 33 208 29 846.0 0 29 209 19 846.0 0 19 210 19 846.0 0 19 211 18 846.0 0 18 212 18 846.0 0 18 213 27 846.0 0 27 214 32 846.0 0 32 215 30 846.0 0 30 216 46 846.0 0 46 217 38 846.0 0 38 218 29 846.0 0 29 219 30 846.0 0 30 220 39 846.0 0 39 221 19 846.0 0 19 222 23 846.0 0 23 223 39 846.0 0 39 224 30 846.0 0 30 225 18 846.0 0 18 226 25 846.0 0 25 227 36 846.0 0 36 228 53 846.0 0 53 229 49 846.0 0 49 230 54 846.0 0 54 231 31 846.0 0 31 232 56 846.0 0 56 233 111 846.0 0 111 234 61 846.0 0 61 235 234 846.0 0 234 236 69 846.0 0 69 237 53 846.0 0 53 238 85 846.0 0 85 239 58 846.0 0 58 240 22 846.0 0 22 241 29 846.0 0 29 242 21 846.0 0 21 243 26 846.0 0 26 244 58 846.0 0 58 245 78 846.0 0 78 246 59 846.0 0 59 247 33 846.0 0 33 248 53 846.0 0 53 249 50 846.0 0 50 250 83 846.0 0 83 251 54 846.0 0 54 252 46 846.0 0 46 253 279 846.0 0 279 254 283 846.0 0 283 255 301 846.0 0 301 256 66 846.0 0 66 257 190 846.0 0 190 258 265 846.0 0 265 259 4878 846.0 0 4878 260 162 846.0 0 162 261 259 846.0 0 259 262 774 846.0 0 774 263 3162 846.0 0 3162 264 887 846.0 0 887 265 503 846.0 0 503 266 43 846.0 0 43 267 38 846.0 0 38 268 24 846.0 0 24 269 17 846.0 0 17 270 23 846.0 0 23 271 12 846.0 0 12 272 25 846.0 0 25 273 30 846.0 0 30 274 39 846.0 0 39 275 26 846.0 0 26 276 25 846.0 0 25 277 117 846.0 0 117 278 73 846.0 0 73 279 57 846.0 0 57 280 42 846.0 0 42 281 51 846.0 0 51 282 52 846.0 0 52 283 66 846.0 0 66 284 102 846.0 0 102 285 210 846.0 0 210 286 98 846.0 0 98 287 166 846.0 0 166 288 156 846.0 0 156 289 134 846.0 0 134 290 103 846.0 0 103 291 163 846.0 0 163 292 345 846.0 0 345 293 581 846.0 0 581 294 172 846.0 0 172 295 133 846.0 0 133 296 188 846.0 0 188 297 325 846.0 0 325 298 4218 846.0 0 4218 299 4998 846.0 0 4998 300 6252 846.0 0 6252 301 93 846.0 0 93 Finished in 1.90 s (45 us/read; 1.32 M reads/minute). === Summary === Total reads processed: 41,939 Reads with adapters: 17,917 (42.7%) Reads that were too short: 10 (0.0%) Reads written (passing filters): 17,907 (42.7%) Total basepairs processed: 10,082,863 bp Total written (filtered): 4,904,916 bp (48.6%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 17917 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 4 0.0 3 0 0 3 0 1 19 89 0.0 3 0 86 2 0 1 20 17124 0.0 4 16965 152 7 21 43 0.0 4 6 37 22 17 0.0 4 1 13 3 23 620 0.0 4 606 7 0 6 1 24 5 0.0 4 2 2 0 0 1 59 1 0.0 4 0 0 0 0 1 70 3 0.0 4 0 0 0 0 3 88 1 0.0 4 0 0 0 0 1 104 1 0.0 4 0 0 0 0 1 119 1 0.0 4 0 0 0 0 1 174 1 0.0 4 0 0 0 0 1 182 1 0.0 4 0 0 0 0 1 185 1 0.0 4 0 0 0 0 1 206 1 0.0 4 0 0 0 0 1 208 1 0.0 4 0 0 0 0 1 223 1 0.0 4 0 0 0 0 1 250 1 0.0 4 0 0 0 0 1 259 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 0.60 s (34 us/read; 1.79 M reads/minute). === Summary === Total reads processed: 17,907 Reads with adapters: 163 (0.9%) Reads written (passing filters): 17,907 (100.0%) Total basepairs processed: 4,904,916 bp Total written (filtered): 4,896,088 bp (99.8%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 163 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 7.4% C: 4.3% G: 85.9% 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 3 279.8 0 3 9 2 0.1 0 1 1 10 12 0.0 1 0 12 11 114 0.0 1 0 114 12 3 0.0 1 0 3 20 1 0.0 1 1 152 1 0.0 1 0 1 261 1 0.0 1 1 262 4 0.0 1 4 263 5 0.0 1 4 1 264 2 0.0 1 2 265 2 0.0 1 2 270 1 0.0 1 1 271 2 0.0 1 2 272 5 0.0 1 5 273 5 0.0 1 4 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.