This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AACAAC -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 103.80 s (33 us/read; 1.84 M reads/minute). === Summary === Total reads processed: 3,184,960 Reads with adapters: 568,459 (17.8%) Reads that were too short: 214,530 (6.7%) Reads written (passing filters): 353,929 (11.1%) Total basepairs processed: 958,672,960 bp Total written (filtered): 66,549,517 bp (6.9%) === Adapter 1 === Sequence: AACAAC; Type: regular 5'; Length: 6; Trimmed: 568459 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 609 777.6 0 609 7 2630 777.6 0 2630 8 56634 777.6 0 56634 9 95 777.6 0 95 10 14 777.6 0 14 11 20 777.6 0 20 12 12 777.6 0 12 13 18 777.6 0 18 14 7 777.6 0 7 15 10 777.6 0 10 16 17 777.6 0 17 17 14 777.6 0 14 18 15 777.6 0 15 19 10 777.6 0 10 20 6 777.6 0 6 21 10 777.6 0 10 22 8 777.6 0 8 23 8 777.6 0 8 24 7 777.6 0 7 25 10 777.6 0 10 26 19 777.6 0 19 27 9 777.6 0 9 28 7 777.6 0 7 29 9 777.6 0 9 30 8 777.6 0 8 31 11 777.6 0 11 32 15 777.6 0 15 33 12 777.6 0 12 34 14 777.6 0 14 35 9 777.6 0 9 36 14 777.6 0 14 37 10 777.6 0 10 38 11 777.6 0 11 39 9 777.6 0 9 40 21 777.6 0 21 41 21 777.6 0 21 42 90 777.6 0 90 43 79 777.6 0 79 44 11 777.6 0 11 45 11 777.6 0 11 46 9 777.6 0 9 47 9 777.6 0 9 48 13 777.6 0 13 49 12 777.6 0 12 50 9 777.6 0 9 51 12 777.6 0 12 52 13 777.6 0 13 53 7 777.6 0 7 54 14 777.6 0 14 55 9 777.6 0 9 56 11 777.6 0 11 57 11 777.6 0 11 58 6 777.6 0 6 59 15 777.6 0 15 60 10 777.6 0 10 61 13 777.6 0 13 62 9 777.6 0 9 63 11 777.6 0 11 64 8 777.6 0 8 65 46 777.6 0 46 66 26 777.6 0 26 67 69 777.6 0 69 68 21 777.6 0 21 69 11 777.6 0 11 70 46 777.6 0 46 71 69 777.6 0 69 72 28 777.6 0 28 73 24 777.6 0 24 74 16 777.6 0 16 75 43 777.6 0 43 76 59 777.6 0 59 77 87 777.6 0 87 78 1016 777.6 0 1016 79 2883 777.6 0 2883 80 3414 777.6 0 3414 81 2938 777.6 0 2938 82 3026 777.6 0 3026 83 5631 777.6 0 5631 84 3327 777.6 0 3327 85 1851 777.6 0 1851 86 2533 777.6 0 2533 87 7763 777.6 0 7763 88 815 777.6 0 815 89 1042 777.6 0 1042 90 8844 777.6 0 8844 91 3946 777.6 0 3946 92 2049 777.6 0 2049 93 2311 777.6 0 2311 94 4327 777.6 0 4327 95 1395 777.6 0 1395 96 1001 777.6 0 1001 97 1944 777.6 0 1944 98 1001 777.6 0 1001 99 925 777.6 0 925 100 2643 777.6 0 2643 101 2094 777.6 0 2094 102 1282 777.6 0 1282 103 2703 777.6 0 2703 104 2823 777.6 0 2823 105 1171 777.6 0 1171 106 2058 777.6 0 2058 107 3215 777.6 0 3215 108 1201 777.6 0 1201 109 1611 777.6 0 1611 110 2950 777.6 0 2950 111 2677 777.6 0 2677 112 2484 777.6 0 2484 113 2689 777.6 0 2689 114 2180 777.6 0 2180 115 2282 777.6 0 2282 116 5976 777.6 0 5976 117 1829 777.6 0 1829 118 1953 777.6 0 1953 119 3463 777.6 0 3463 120 2608 777.6 0 2608 121 2112 777.6 0 2112 122 3107 777.6 0 3107 123 2391 777.6 0 2391 124 2493 777.6 0 2493 125 2879 777.6 0 2879 126 2731 777.6 0 2731 127 2150 777.6 0 2150 128 3144 777.6 0 3144 129 2064 777.6 0 2064 130 1931 777.6 0 1931 131 3279 777.6 0 3279 132 2556 777.6 0 2556 133 2044 777.6 0 2044 134 1789 777.6 0 1789 135 1770 777.6 0 1770 136 1679 777.6 0 1679 137 1816 777.6 0 1816 138 1791 777.6 0 1791 139 1609 777.6 0 1609 140 1490 777.6 0 1490 141 2138 777.6 0 2138 142 2864 777.6 0 2864 143 1686 777.6 0 1686 144 1929 777.6 0 1929 145 2649 777.6 0 2649 146 2445 777.6 0 2445 147 2065 777.6 0 2065 148 1937 777.6 0 1937 149 2609 777.6 0 2609 150 3278 777.6 0 3278 151 3731 777.6 0 3731 152 3133 777.6 0 3133 153 3147 777.6 0 3147 154 4172 777.6 0 4172 155 2756 777.6 0 2756 156 1958 777.6 0 1958 157 2363 777.6 0 2363 158 2180 777.6 0 2180 159 2129 777.6 0 2129 160 1958 777.6 0 1958 161 2109 777.6 0 2109 162 2698 777.6 0 2698 163 2028 777.6 0 2028 164 1674 777.6 0 1674 165 1568 777.6 0 1568 166 1475 777.6 0 1475 167 1582 777.6 0 1582 168 1469 777.6 0 1469 169 1601 777.6 0 1601 170 2968 777.6 0 2968 171 2656 777.6 0 2656 172 1461 777.6 0 1461 173 2713 777.6 0 2713 174 2046 777.6 0 2046 175 1836 777.6 0 1836 176 2044 777.6 0 2044 177 2423 777.6 0 2423 178 2869 777.6 0 2869 179 2840 777.6 0 2840 180 2285 777.6 0 2285 181 2122 777.6 0 2122 182 2054 777.6 0 2054 183 1875 777.6 0 1875 184 1361 777.6 0 1361 185 1260 777.6 0 1260 186 1505 777.6 0 1505 187 1886 777.6 0 1886 188 2252 777.6 0 2252 189 2100 777.6 0 2100 190 2231 777.6 0 2231 191 2680 777.6 0 2680 192 1918 777.6 0 1918 193 1245 777.6 0 1245 194 2240 777.6 0 2240 195 2264 777.6 0 2264 196 1178 777.6 0 1178 197 1611 777.6 0 1611 198 1854 777.6 0 1854 199 1653 777.6 0 1653 200 1788 777.6 0 1788 201 1391 777.6 0 1391 202 1321 777.6 0 1321 203 1999 777.6 0 1999 204 2014 777.6 0 2014 205 1151 777.6 0 1151 206 1205 777.6 0 1205 207 1423 777.6 0 1423 208 1187 777.6 0 1187 209 1356 777.6 0 1356 210 1496 777.6 0 1496 211 1483 777.6 0 1483 212 1670 777.6 0 1670 213 2096 777.6 0 2096 214 1804 777.6 0 1804 215 2023 777.6 0 2023 216 1538 777.6 0 1538 217 1780 777.6 0 1780 218 1405 777.6 0 1405 219 1579 777.6 0 1579 220 1789 777.6 0 1789 221 1593 777.6 0 1593 222 1141 777.6 0 1141 223 1858 777.6 0 1858 224 2157 777.6 0 2157 225 2080 777.6 0 2080 226 2722 777.6 0 2722 227 2011 777.6 0 2011 228 2416 777.6 0 2416 229 2500 777.6 0 2500 230 2643 777.6 0 2643 231 4019 777.6 0 4019 232 4569 777.6 0 4569 233 1680 777.6 0 1680 234 1590 777.6 0 1590 235 2321 777.6 0 2321 236 1305 777.6 0 1305 237 1044 777.6 0 1044 238 1144 777.6 0 1144 239 1421 777.6 0 1421 240 1599 777.6 0 1599 241 1780 777.6 0 1780 242 1595 777.6 0 1595 243 1783 777.6 0 1783 244 1690 777.6 0 1690 245 1411 777.6 0 1411 246 1066 777.6 0 1066 247 1321 777.6 0 1321 248 1426 777.6 0 1426 249 1688 777.6 0 1688 250 1723 777.6 0 1723 251 2035 777.6 0 2035 252 2742 777.6 0 2742 253 2288 777.6 0 2288 254 1432 777.6 0 1432 255 1179 777.6 0 1179 256 1141 777.6 0 1141 257 1048 777.6 0 1048 258 1173 777.6 0 1173 259 1095 777.6 0 1095 260 1652 777.6 0 1652 261 1917 777.6 0 1917 262 2345 777.6 0 2345 263 9106 777.6 0 9106 264 20841 777.6 0 20841 265 10318 777.6 0 10318 266 11685 777.6 0 11685 267 1506 777.6 0 1506 268 1565 777.6 0 1565 269 1294 777.6 0 1294 270 1516 777.6 0 1516 271 1877 777.6 0 1877 272 1728 777.6 0 1728 273 1644 777.6 0 1644 274 1671 777.6 0 1671 275 1946 777.6 0 1946 276 1644 777.6 0 1644 277 1528 777.6 0 1528 278 1696 777.6 0 1696 279 1520 777.6 0 1520 280 2002 777.6 0 2002 281 1526 777.6 0 1526 282 982 777.6 0 982 283 1794 777.6 0 1794 284 1631 777.6 0 1631 285 1234 777.6 0 1234 286 1058 777.6 0 1058 287 1142 777.6 0 1142 288 1383 777.6 0 1383 289 1934 777.6 0 1934 290 3415 777.6 0 3415 291 2311 777.6 0 2311 292 1948 777.6 0 1948 293 1651 777.6 0 1651 294 1272 777.6 0 1272 295 954 777.6 0 954 296 1225 777.6 0 1225 297 1489 777.6 0 1489 298 1587 777.6 0 1587 299 1354 777.6 0 1354 300 1414 777.6 0 1414 301 477 777.6 0 477 Finished in 15.65 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 353,929 Reads with adapters: 59,868 (16.9%) Reads that were too short: 48 (0.0%) Reads written (passing filters): 59,820 (16.9%) Total basepairs processed: 66,549,517 bp Total written (filtered): 16,330,327 bp (24.5%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 59868 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 2 0.0 3 0 0 0 0 2 17 2 0.0 3 0 0 0 1 1 18 23 0.0 3 0 0 22 1 19 753 0.0 3 0 728 17 4 4 20 58542 0.0 4 57593 917 25 6 1 21 184 0.0 4 29 153 1 0 1 22 13 0.0 4 1 2 9 0 1 23 271 0.0 4 244 4 0 19 4 24 2 0.0 4 1 0 0 0 1 25 1 0.0 4 0 0 0 1 26 2 0.0 4 0 0 0 0 2 28 1 0.0 4 0 0 0 0 1 30 1 0.0 4 1 31 1 0.0 4 0 0 0 0 1 33 1 0.0 4 0 0 0 0 1 35 1 0.0 4 1 36 5 0.0 4 0 0 0 0 5 37 1 0.0 4 0 0 0 0 1 38 1 0.0 4 0 0 0 0 1 39 1 0.0 4 0 0 0 0 1 43 3 0.0 4 0 0 0 0 3 46 2 0.0 4 0 0 0 0 2 50 1 0.0 4 0 0 0 0 1 52 2 0.0 4 0 0 0 0 2 53 1 0.0 4 0 0 0 0 1 55 1 0.0 4 0 0 0 0 1 57 1 0.0 4 0 0 0 0 1 58 1 0.0 4 0 0 0 0 1 59 1 0.0 4 0 0 0 0 1 60 1 0.0 4 0 0 0 0 1 63 1 0.0 4 0 0 0 0 1 64 1 0.0 4 0 0 0 0 1 65 1 0.0 4 0 0 0 0 1 67 1 0.0 4 0 0 0 0 1 71 2 0.0 4 0 0 0 0 2 75 1 0.0 4 0 0 0 0 1 77 1 0.0 4 0 0 0 0 1 79 3 0.0 4 0 0 0 0 3 81 1 0.0 4 0 0 0 0 1 89 1 0.0 4 0 0 0 0 1 91 2 0.0 4 0 0 0 0 2 92 1 0.0 4 0 0 0 0 1 97 1 0.0 4 0 0 0 0 1 103 1 0.0 4 0 0 0 0 1 106 1 0.0 4 0 0 0 0 1 108 2 0.0 4 0 0 0 0 2 110 1 0.0 4 0 0 0 0 1 113 2 0.0 4 0 0 0 0 2 115 1 0.0 4 0 0 0 0 1 118 1 0.0 4 0 0 0 0 1 119 1 0.0 4 0 0 0 1 120 1 0.0 4 0 0 0 0 1 121 1 0.0 4 0 0 0 0 1 122 1 0.0 4 0 0 0 0 1 130 1 0.0 4 0 0 0 0 1 132 1 0.0 4 0 0 0 0 1 134 1 0.0 4 0 0 0 0 1 137 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 1 142 1 0.0 4 0 0 0 0 1 143 1 0.0 4 0 0 0 0 1 145 1 0.0 4 0 0 0 0 1 147 1 0.0 4 0 0 0 0 1 152 1 0.0 4 0 0 0 0 1 153 1 0.0 4 0 0 0 0 1 157 1 0.0 4 0 0 0 0 1 165 1 0.0 4 0 0 0 0 1 177 1 0.0 4 0 0 0 0 1 184 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 2.52 s (42 us/read; 1.42 M reads/minute). === Summary === Total reads processed: 59,820 Reads with adapters: 1,811 (3.0%) Reads written (passing filters): 59,820 (100.0%) Total basepairs processed: 16,330,327 bp Total written (filtered): 16,308,514 bp (99.9%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 1811 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.0% C: 0.3% G: 97.6% T: 1.0% 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 2 934.7 0 2 4 20 233.7 0 20 5 4 58.4 0 4 6 1 14.6 0 1 10 26 0.1 1 1 25 11 1747 0.0 1 2 1745 170 1 0.0 1 1 190 2 0.0 1 0 2 209 7 0.0 1 5 2 211 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.