This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g ACACAA -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 100.98 s (33 us/read; 1.84 M reads/minute). === Summary === Total reads processed: 3,094,653 Reads with adapters: 599,108 (19.4%) Reads that were too short: 228,820 (7.4%) Reads written (passing filters): 370,288 (12.0%) Total basepairs processed: 931,490,553 bp Total written (filtered): 62,737,399 bp (6.7%) === Adapter 1 === Sequence: ACACAA; Type: regular 5'; Length: 6; Trimmed: 599108 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 3530 755.5 0 3530 7 3455 755.5 0 3455 8 146 755.5 0 146 9 6070 755.5 0 6070 10 14 755.5 0 14 11 6 755.5 0 6 12 3 755.5 0 3 13 4 755.5 0 4 14 6 755.5 0 6 15 10 755.5 0 10 16 4 755.5 0 4 17 10 755.5 0 10 18 4 755.5 0 4 19 6 755.5 0 6 20 4 755.5 0 4 21 5 755.5 0 5 22 10 755.5 0 10 23 3 755.5 0 3 24 3 755.5 0 3 25 6 755.5 0 6 26 16 755.5 0 16 27 8 755.5 0 8 28 15 755.5 0 15 29 11 755.5 0 11 30 22 755.5 0 22 31 18 755.5 0 18 32 44 755.5 0 44 33 26 755.5 0 26 34 17 755.5 0 17 35 7 755.5 0 7 36 129 755.5 0 129 37 9 755.5 0 9 38 43 755.5 0 43 39 10 755.5 0 10 40 17 755.5 0 17 41 64 755.5 0 64 42 50 755.5 0 50 43 176 755.5 0 176 44 10 755.5 0 10 45 3 755.5 0 3 46 8 755.5 0 8 47 6 755.5 0 6 48 9 755.5 0 9 49 11 755.5 0 11 50 6 755.5 0 6 51 10 755.5 0 10 52 16 755.5 0 16 53 8 755.5 0 8 54 3 755.5 0 3 55 11 755.5 0 11 56 9 755.5 0 9 57 15 755.5 0 15 58 15 755.5 0 15 59 38 755.5 0 38 60 12 755.5 0 12 61 9 755.5 0 9 62 6 755.5 0 6 63 9 755.5 0 9 64 12 755.5 0 12 65 3 755.5 0 3 66 6 755.5 0 6 67 12 755.5 0 12 68 43 755.5 0 43 69 313 755.5 0 313 70 29 755.5 0 29 71 51 755.5 0 51 72 38 755.5 0 38 73 53 755.5 0 53 74 52 755.5 0 52 75 108 755.5 0 108 76 101 755.5 0 101 77 557 755.5 0 557 78 1364 755.5 0 1364 79 2097 755.5 0 2097 80 2638 755.5 0 2638 81 3703 755.5 0 3703 82 3776 755.5 0 3776 83 3599 755.5 0 3599 84 3673 755.5 0 3673 85 4685 755.5 0 4685 86 3658 755.5 0 3658 87 1726 755.5 0 1726 88 1617 755.5 0 1617 89 3471 755.5 0 3471 90 1492 755.5 0 1492 91 7572 755.5 0 7572 92 891 755.5 0 891 93 3394 755.5 0 3394 94 2221 755.5 0 2221 95 6781 755.5 0 6781 96 3116 755.5 0 3116 97 1473 755.5 0 1473 98 542 755.5 0 542 99 1160 755.5 0 1160 100 936 755.5 0 936 101 2400 755.5 0 2400 102 2293 755.5 0 2293 103 2891 755.5 0 2891 104 1902 755.5 0 1902 105 6423 755.5 0 6423 106 4549 755.5 0 4549 107 4166 755.5 0 4166 108 2081 755.5 0 2081 109 2006 755.5 0 2006 110 1850 755.5 0 1850 111 4518 755.5 0 4518 112 3366 755.5 0 3366 113 4819 755.5 0 4819 114 3292 755.5 0 3292 115 4173 755.5 0 4173 116 1402 755.5 0 1402 117 2253 755.5 0 2253 118 2363 755.5 0 2363 119 2936 755.5 0 2936 120 3218 755.5 0 3218 121 3579 755.5 0 3579 122 2544 755.5 0 2544 123 3231 755.5 0 3231 124 3271 755.5 0 3271 125 4125 755.5 0 4125 126 5061 755.5 0 5061 127 3819 755.5 0 3819 128 3233 755.5 0 3233 129 1689 755.5 0 1689 130 2776 755.5 0 2776 131 1700 755.5 0 1700 132 3532 755.5 0 3532 133 5652 755.5 0 5652 134 3846 755.5 0 3846 135 3426 755.5 0 3426 136 2291 755.5 0 2291 137 2159 755.5 0 2159 138 1929 755.5 0 1929 139 2222 755.5 0 2222 140 2741 755.5 0 2741 141 3423 755.5 0 3423 142 2113 755.5 0 2113 143 2332 755.5 0 2332 144 2138 755.5 0 2138 145 3371 755.5 0 3371 146 4142 755.5 0 4142 147 2766 755.5 0 2766 148 4039 755.5 0 4039 149 3320 755.5 0 3320 150 4024 755.5 0 4024 151 2482 755.5 0 2482 152 3278 755.5 0 3278 153 4005 755.5 0 4005 154 3790 755.5 0 3790 155 2812 755.5 0 2812 156 2665 755.5 0 2665 157 2011 755.5 0 2011 158 2592 755.5 0 2592 159 2366 755.5 0 2366 160 2835 755.5 0 2835 161 3256 755.5 0 3256 162 4143 755.5 0 4143 163 4342 755.5 0 4342 164 3701 755.5 0 3701 165 3112 755.5 0 3112 166 2253 755.5 0 2253 167 1839 755.5 0 1839 168 1824 755.5 0 1824 169 2419 755.5 0 2419 170 2404 755.5 0 2404 171 1889 755.5 0 1889 172 3257 755.5 0 3257 173 2311 755.5 0 2311 174 4917 755.5 0 4917 175 2113 755.5 0 2113 176 1755 755.5 0 1755 177 1263 755.5 0 1263 178 2176 755.5 0 2176 179 2331 755.5 0 2331 180 2897 755.5 0 2897 181 2549 755.5 0 2549 182 1904 755.5 0 1904 183 2123 755.5 0 2123 184 1957 755.5 0 1957 185 2455 755.5 0 2455 186 3025 755.5 0 3025 187 2604 755.5 0 2604 188 2351 755.5 0 2351 189 1871 755.5 0 1871 190 2714 755.5 0 2714 191 3144 755.5 0 3144 192 3272 755.5 0 3272 193 2742 755.5 0 2742 194 2023 755.5 0 2023 195 1015 755.5 0 1015 196 1322 755.5 0 1322 197 1375 755.5 0 1375 198 2572 755.5 0 2572 199 4140 755.5 0 4140 200 1992 755.5 0 1992 201 1547 755.5 0 1547 202 1491 755.5 0 1491 203 1588 755.5 0 1588 204 1689 755.5 0 1689 205 2056 755.5 0 2056 206 2019 755.5 0 2019 207 1773 755.5 0 1773 208 1672 755.5 0 1672 209 1657 755.5 0 1657 210 1678 755.5 0 1678 211 2239 755.5 0 2239 212 3051 755.5 0 3051 213 19454 755.5 0 19454 214 7654 755.5 0 7654 215 6920 755.5 0 6920 216 1888 755.5 0 1888 217 1886 755.5 0 1886 218 2434 755.5 0 2434 219 2720 755.5 0 2720 220 2012 755.5 0 2012 221 1422 755.5 0 1422 222 1735 755.5 0 1735 223 1458 755.5 0 1458 224 2293 755.5 0 2293 225 2435 755.5 0 2435 226 2283 755.5 0 2283 227 2901 755.5 0 2901 228 2001 755.5 0 2001 229 2379 755.5 0 2379 230 2596 755.5 0 2596 231 2263 755.5 0 2263 232 1303 755.5 0 1303 233 1364 755.5 0 1364 234 1900 755.5 0 1900 235 1955 755.5 0 1955 236 2319 755.5 0 2319 237 2283 755.5 0 2283 238 2325 755.5 0 2325 239 2700 755.5 0 2700 240 2110 755.5 0 2110 241 1482 755.5 0 1482 242 1486 755.5 0 1486 243 1405 755.5 0 1405 244 1397 755.5 0 1397 245 1955 755.5 0 1955 246 2417 755.5 0 2417 247 3529 755.5 0 3529 248 2931 755.5 0 2931 249 2540 755.5 0 2540 250 2730 755.5 0 2730 251 2432 755.5 0 2432 252 1820 755.5 0 1820 253 2027 755.5 0 2027 254 1701 755.5 0 1701 255 2295 755.5 0 2295 256 2434 755.5 0 2434 257 3068 755.5 0 3068 258 2103 755.5 0 2103 259 2139 755.5 0 2139 260 1268 755.5 0 1268 261 1249 755.5 0 1249 262 1320 755.5 0 1320 263 1237 755.5 0 1237 264 1545 755.5 0 1545 265 1672 755.5 0 1672 266 1996 755.5 0 1996 267 2731 755.5 0 2731 268 2240 755.5 0 2240 269 2365 755.5 0 2365 270 1701 755.5 0 1701 271 1522 755.5 0 1522 272 1676 755.5 0 1676 273 2008 755.5 0 2008 274 2136 755.5 0 2136 275 1887 755.5 0 1887 276 1651 755.5 0 1651 277 1369 755.5 0 1369 278 1546 755.5 0 1546 279 2352 755.5 0 2352 280 2334 755.5 0 2334 281 1420 755.5 0 1420 282 1850 755.5 0 1850 283 1193 755.5 0 1193 284 2173 755.5 0 2173 285 1928 755.5 0 1928 286 2432 755.5 0 2432 287 2564 755.5 0 2564 288 1831 755.5 0 1831 289 1830 755.5 0 1830 290 1377 755.5 0 1377 291 4031 755.5 0 4031 292 1808 755.5 0 1808 293 2372 755.5 0 2372 294 2070 755.5 0 2070 295 2127 755.5 0 2127 296 1374 755.5 0 1374 297 1127 755.5 0 1127 298 706 755.5 0 706 299 768 755.5 0 768 300 1184 755.5 0 1184 301 5053 755.5 0 5053 Finished in 15.57 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 370,288 Reads with adapters: 6,947 (1.9%) Reads that were too short: 60 (0.0%) Reads written (passing filters): 6,887 (1.9%) Total basepairs processed: 62,737,399 bp Total written (filtered): 1,880,519 bp (3.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 6947 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 5 0.0 3 0 0 0 0 5 18 2 0.0 3 0 0 2 19 71 0.0 3 0 70 1 20 3407 0.0 4 3350 54 1 1 1 21 67 0.0 4 6 60 0 0 1 22 3299 0.0 4 3246 48 4 0 1 23 8 0.0 4 0 6 1 1 24 4 0.0 4 0 0 1 0 3 25 4 0.0 4 0 0 0 3 1 26 1 0.0 4 1 31 1 0.0 4 0 0 0 0 1 32 2 0.0 4 0 0 0 1 1 37 1 0.0 4 0 0 0 1 42 2 0.0 4 0 0 0 0 2 43 2 0.0 4 0 0 0 0 2 44 1 0.0 4 0 0 0 0 1 46 1 0.0 4 0 0 0 0 1 50 1 0.0 4 0 0 0 0 1 53 2 0.0 4 0 0 0 0 2 54 2 0.0 4 0 0 0 0 2 57 1 0.0 4 0 0 0 0 1 59 2 0.0 4 0 0 0 0 2 60 1 0.0 4 0 0 0 0 1 61 2 0.0 4 0 0 0 0 2 64 1 0.0 4 0 0 0 0 1 65 1 0.0 4 0 0 0 0 1 69 1 0.0 4 0 0 0 0 1 70 1 0.0 4 0 0 0 0 1 74 1 0.0 4 0 0 0 0 1 76 1 0.0 4 0 0 0 0 1 78 3 0.0 4 0 0 0 1 2 80 1 0.0 4 0 0 0 0 1 82 2 0.0 4 0 0 0 0 2 85 1 0.0 4 0 0 0 0 1 93 1 0.0 4 0 0 0 0 1 103 1 0.0 4 0 0 0 0 1 108 2 0.0 4 0 0 0 0 2 116 2 0.0 4 0 0 0 0 2 124 1 0.0 4 0 0 0 0 1 125 2 0.0 4 0 0 0 0 2 126 1 0.0 4 0 0 0 0 1 127 1 0.0 4 0 0 0 0 1 128 1 0.0 4 0 0 0 0 1 133 1 0.0 4 0 0 0 0 1 138 1 0.0 4 0 0 0 0 1 139 1 0.0 4 0 0 0 0 1 140 1 0.0 4 0 0 0 0 1 141 2 0.0 4 0 0 0 0 2 144 1 0.0 4 0 0 0 0 1 147 1 0.0 4 0 0 0 0 1 149 1 0.0 4 0 0 0 0 1 150 1 0.0 4 0 0 0 0 1 153 4 0.0 4 0 0 0 0 4 154 1 0.0 4 0 0 0 0 1 156 1 0.0 4 0 0 0 0 1 157 1 0.0 4 0 0 0 0 1 161 1 0.0 4 0 0 0 0 1 162 1 0.0 4 0 0 0 0 1 163 1 0.0 4 0 0 0 0 1 165 1 0.0 4 0 0 0 0 1 166 1 0.0 4 0 0 0 0 1 167 1 0.0 4 0 0 0 0 1 168 3 0.0 4 0 0 0 0 3 169 1 0.0 4 0 0 0 0 1 177 1 0.0 4 0 0 0 0 1 186 1 0.0 4 0 0 0 0 1 187 2 0.0 4 0 0 0 0 2 205 1 0.0 4 0 0 0 0 1 281 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 0.28 s (41 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 6,887 Reads with adapters: 2,148 (31.2%) Reads written (passing filters): 6,887 (100.0%) Total basepairs processed: 1,880,519 bp Total written (filtered): 1,326,825 bp (70.6%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 2148 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 98.5% C: 0.0% G: 1.3% T: 0.1% none/other: 0.0% WARNING: The adapter is preceded by "A" extremely often. The provided adapter sequence may be incomplete. To fix the problem, add "A" to the beginning of the adapter sequence. Overview of removed sequences length count expect max.err error counts 10 5 0.0 1 0 5 11 23 0.0 1 0 23 234 3 0.0 1 3 258 1 0.0 1 1 260 5 0.0 1 5 261 1986 0.0 1 1840 146 262 117 0.0 1 101 16 263 3 0.0 1 3 265 2 0.0 1 2 269 2 0.0 1 2 274 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.