This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TCCAGC -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 59.46 s (27 us/read; 2.21 M reads/minute). === Summary === Total reads processed: 2,192,295 Reads with adapters: 406,459 (18.5%) Reads that were too short: 10,324 (0.5%) Reads written (passing filters): 396,135 (18.1%) Total basepairs processed: 659,880,795 bp Total written (filtered): 88,631,282 bp (13.4%) === Adapter 1 === Sequence: TCCAGC; Type: regular 5'; Length: 6; Trimmed: 406459 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 289 535.2 0 289 7 478 535.2 0 478 8 8234 535.2 0 8234 9 8782 535.2 0 8782 10 83 535.2 0 83 11 83 535.2 0 83 12 78 535.2 0 78 13 72 535.2 0 72 14 77 535.2 0 77 15 60 535.2 0 60 16 58 535.2 0 58 17 68 535.2 0 68 18 87 535.2 0 87 19 108 535.2 0 108 20 104 535.2 0 104 21 84 535.2 0 84 22 97 535.2 0 97 23 100 535.2 0 100 24 138 535.2 0 138 25 61 535.2 0 61 26 82 535.2 0 82 27 102 535.2 0 102 28 64 535.2 0 64 29 96 535.2 0 96 30 135 535.2 0 135 31 84 535.2 0 84 32 123 535.2 0 123 33 82 535.2 0 82 34 115 535.2 0 115 35 107 535.2 0 107 36 226 535.2 0 226 37 202 535.2 0 202 38 479 535.2 0 479 39 211 535.2 0 211 40 135 535.2 0 135 41 91 535.2 0 91 42 208 535.2 0 208 43 111 535.2 0 111 44 190 535.2 0 190 45 263 535.2 0 263 46 250 535.2 0 250 47 346 535.2 0 346 48 760 535.2 0 760 49 1614 535.2 0 1614 50 420 535.2 0 420 51 515 535.2 0 515 52 987 535.2 0 987 53 488 535.2 0 488 54 494 535.2 0 494 55 1059 535.2 0 1059 56 1147 535.2 0 1147 57 1263 535.2 0 1263 58 1370 535.2 0 1370 59 2433 535.2 0 2433 60 2206 535.2 0 2206 61 3118 535.2 0 3118 62 61624 535.2 0 61624 63 116552 535.2 0 116552 64 97426 535.2 0 97426 65 578 535.2 0 578 66 76 535.2 0 76 67 51 535.2 0 51 68 49 535.2 0 49 69 68 535.2 0 68 70 85 535.2 0 85 71 273 535.2 0 273 72 309 535.2 0 309 73 424 535.2 0 424 74 129 535.2 0 129 75 157 535.2 0 157 76 2547 535.2 0 2547 77 1641 535.2 0 1641 78 1192 535.2 0 1192 79 184 535.2 0 184 80 73 535.2 0 73 81 52 535.2 0 52 82 67 535.2 0 67 83 73 535.2 0 73 84 61 535.2 0 61 85 70 535.2 0 70 86 74 535.2 0 74 87 67 535.2 0 67 88 44 535.2 0 44 89 57 535.2 0 57 90 48 535.2 0 48 91 62 535.2 0 62 92 53 535.2 0 53 93 86 535.2 0 86 94 80 535.2 0 80 95 61 535.2 0 61 96 54 535.2 0 54 97 61 535.2 0 61 98 50 535.2 0 50 99 89 535.2 0 89 100 110 535.2 0 110 101 59 535.2 0 59 102 53 535.2 0 53 103 50 535.2 0 50 104 110 535.2 0 110 105 62 535.2 0 62 106 137 535.2 0 137 107 291 535.2 0 291 108 187 535.2 0 187 109 310 535.2 0 310 110 91 535.2 0 91 111 92 535.2 0 92 112 99 535.2 0 99 113 84 535.2 0 84 114 64 535.2 0 64 115 73 535.2 0 73 116 51 535.2 0 51 117 91 535.2 0 91 118 66 535.2 0 66 119 74 535.2 0 74 120 68 535.2 0 68 121 61 535.2 0 61 122 58 535.2 0 58 123 58 535.2 0 58 124 102 535.2 0 102 125 78 535.2 0 78 126 115 535.2 0 115 127 179 535.2 0 179 128 97 535.2 0 97 129 136 535.2 0 136 130 73 535.2 0 73 131 63 535.2 0 63 132 107 535.2 0 107 133 79 535.2 0 79 134 113 535.2 0 113 135 66 535.2 0 66 136 84 535.2 0 84 137 133 535.2 0 133 138 107 535.2 0 107 139 130 535.2 0 130 140 209 535.2 0 209 141 176 535.2 0 176 142 351 535.2 0 351 143 488 535.2 0 488 144 6690 535.2 0 6690 145 4314 535.2 0 4314 146 5471 535.2 0 5471 147 219 535.2 0 219 148 107 535.2 0 107 149 106 535.2 0 106 150 106 535.2 0 106 151 105 535.2 0 105 152 157 535.2 0 157 153 195 535.2 0 195 154 175 535.2 0 175 155 128 535.2 0 128 156 557 535.2 0 557 157 604 535.2 0 604 158 1349 535.2 0 1349 159 217 535.2 0 217 160 224 535.2 0 224 161 306 535.2 0 306 162 551 535.2 0 551 163 1285 535.2 0 1285 164 15014 535.2 0 15014 165 11630 535.2 0 11630 166 8547 535.2 0 8547 167 132 535.2 0 132 168 94 535.2 0 94 169 257 535.2 0 257 170 402 535.2 0 402 171 1445 535.2 0 1445 172 694 535.2 0 694 173 203 535.2 0 203 174 234 535.2 0 234 175 200 535.2 0 200 176 55 535.2 0 55 177 64 535.2 0 64 178 85 535.2 0 85 179 339 535.2 0 339 180 240 535.2 0 240 181 276 535.2 0 276 182 147 535.2 0 147 183 134 535.2 0 134 184 93 535.2 0 93 185 118 535.2 0 118 186 125 535.2 0 125 187 61 535.2 0 61 188 66 535.2 0 66 189 214 535.2 0 214 190 493 535.2 0 493 191 410 535.2 0 410 192 209 535.2 0 209 193 67 535.2 0 67 194 51 535.2 0 51 195 58 535.2 0 58 196 74 535.2 0 74 197 101 535.2 0 101 198 66 535.2 0 66 199 92 535.2 0 92 200 77 535.2 0 77 201 53 535.2 0 53 202 79 535.2 0 79 203 85 535.2 0 85 204 93 535.2 0 93 205 78 535.2 0 78 206 83 535.2 0 83 207 52 535.2 0 52 208 62 535.2 0 62 209 69 535.2 0 69 210 64 535.2 0 64 211 52 535.2 0 52 212 62 535.2 0 62 213 67 535.2 0 67 214 88 535.2 0 88 215 81 535.2 0 81 216 111 535.2 0 111 217 124 535.2 0 124 218 130 535.2 0 130 219 84 535.2 0 84 220 66 535.2 0 66 221 58 535.2 0 58 222 53 535.2 0 53 223 62 535.2 0 62 224 68 535.2 0 68 225 66 535.2 0 66 226 113 535.2 0 113 227 115 535.2 0 115 228 127 535.2 0 127 229 327 535.2 0 327 230 146 535.2 0 146 231 171 535.2 0 171 232 67 535.2 0 67 233 66 535.2 0 66 234 39 535.2 0 39 235 71 535.2 0 71 236 82 535.2 0 82 237 80 535.2 0 80 238 104 535.2 0 104 239 75 535.2 0 75 240 92 535.2 0 92 241 75 535.2 0 75 242 79 535.2 0 79 243 82 535.2 0 82 244 67 535.2 0 67 245 70 535.2 0 70 246 69 535.2 0 69 247 76 535.2 0 76 248 71 535.2 0 71 249 74 535.2 0 74 250 74 535.2 0 74 251 62 535.2 0 62 252 69 535.2 0 69 253 61 535.2 0 61 254 67 535.2 0 67 255 60 535.2 0 60 256 56 535.2 0 56 257 46 535.2 0 46 258 53 535.2 0 53 259 71 535.2 0 71 260 136 535.2 0 136 261 131 535.2 0 131 262 152 535.2 0 152 263 75 535.2 0 75 264 71 535.2 0 71 265 99 535.2 0 99 266 93 535.2 0 93 267 147 535.2 0 147 268 108 535.2 0 108 269 75 535.2 0 75 270 76 535.2 0 76 271 86 535.2 0 86 272 90 535.2 0 90 273 92 535.2 0 92 274 93 535.2 0 93 275 80 535.2 0 80 276 123 535.2 0 123 277 601 535.2 0 601 278 322 535.2 0 322 279 312 535.2 0 312 280 106 535.2 0 106 281 99 535.2 0 99 282 88 535.2 0 88 283 156 535.2 0 156 284 69 535.2 0 69 285 87 535.2 0 87 286 130 535.2 0 130 287 301 535.2 0 301 288 239 535.2 0 239 289 228 535.2 0 228 290 133 535.2 0 133 291 93 535.2 0 93 292 78 535.2 0 78 293 99 535.2 0 99 294 78 535.2 0 78 295 84 535.2 0 84 296 67 535.2 0 67 297 72 535.2 0 72 298 127 535.2 0 127 299 79 535.2 0 79 300 75 535.2 0 75 301 80 535.2 0 80 Finished in 17.17 s (43 us/read; 1.38 M reads/minute). === Summary === Total reads processed: 396,135 Reads with adapters: 17,275 (4.4%) Reads that were too short: 89 (0.0%) Reads written (passing filters): 17,186 (4.3%) Total basepairs processed: 88,631,282 bp Total written (filtered): 3,854,303 bp (4.3%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 17275 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 7 0.0 3 0 0 7 19 108 0.0 3 0 107 1 20 9243 0.0 4 9095 143 4 0 1 21 25 0.0 4 3 21 0 1 23 14 0.0 4 1 1 0 11 1 24 1 0.0 4 0 0 0 0 1 28 1 0.0 4 0 0 0 0 1 34 8 0.0 4 0 0 0 0 8 37 1 0.0 4 0 0 0 0 1 51 1 0.0 4 0 0 0 0 1 69 2 0.0 4 0 0 0 0 2 70 12 0.0 4 0 0 0 0 12 71 10 0.0 4 0 0 0 0 10 72 7702 0.0 4 0 0 0 0 7702 74 3 0.0 4 0 0 0 0 3 75 4 0.0 4 0 0 0 1 3 81 1 0.0 4 0 0 0 0 1 85 1 0.0 4 0 0 0 0 1 97 1 0.0 4 1 98 1 0.0 4 0 0 0 0 1 101 1 0.0 4 0 0 0 0 1 109 1 0.0 4 1 115 2 0.0 4 2 116 1 0.0 4 0 1 127 36 0.0 4 0 0 0 0 36 128 1 0.0 4 0 0 0 0 1 131 1 0.0 4 0 0 0 0 1 148 1 0.0 4 0 0 0 0 1 150 1 0.0 4 1 157 1 0.0 4 0 0 0 0 1 159 1 0.0 4 0 1 164 1 0.0 4 0 1 166 2 0.0 4 1 0 0 0 1 168 1 0.0 4 0 0 0 0 1 170 1 0.0 4 0 0 0 0 1 171 1 0.0 4 0 0 0 0 1 173 26 0.0 4 0 0 0 0 26 174 4 0.0 4 0 0 0 0 4 177 2 0.0 4 0 0 0 0 2 178 1 0.0 4 0 0 0 0 1 179 1 0.0 4 0 1 180 5 0.0 4 0 0 0 0 5 181 1 0.0 4 0 0 0 0 1 187 2 0.0 4 0 0 0 0 2 188 1 0.0 4 0 0 0 0 1 193 1 0.0 4 0 0 1 202 2 0.0 4 0 0 0 0 2 207 1 0.0 4 0 0 0 0 1 225 1 0.0 4 1 227 9 0.0 4 0 0 0 0 9 228 1 0.0 4 0 0 0 0 1 229 4 0.0 4 0 0 0 0 4 230 3 0.0 4 0 0 0 0 3 233 5 0.0 4 0 0 0 0 5 235 1 0.0 4 0 0 0 0 1 236 3 0.0 4 0 0 1 0 2 237 1 0.0 4 0 0 0 0 1 241 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 0.54 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 17,186 Reads with adapters: 2,127 (12.4%) Reads written (passing filters): 17,186 (100.0%) Total basepairs processed: 3,854,303 bp Total written (filtered): 3,834,494 bp (99.5%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2127 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 3.3% C: 1.9% G: 94.0% T: 0.8% 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 26 268.5 0 26 4 32 67.1 0 32 5 8 16.8 0 8 9 1421 0.1 0 47 1374 10 501 0.0 1 18 483 11 134 0.0 1 1 133 12 3 0.0 1 1 2 79 1 0.0 1 1 175 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.