This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CCGGAA -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 102.33 s (32 us/read; 1.87 M reads/minute). === Summary === Total reads processed: 3,184,960 Reads with adapters: 696,676 (21.9%) Reads that were too short: 554,797 (17.4%) Reads written (passing filters): 141,879 (4.5%) Total basepairs processed: 958,672,960 bp Total written (filtered): 27,026,137 bp (2.8%) === Adapter 1 === Sequence: CCGGAA; Type: regular 5'; Length: 6; Trimmed: 696676 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 920 777.6 0 920 7 40542 777.6 0 40542 8 165 777.6 0 165 9 72 777.6 0 72 10 11 777.6 0 11 11 14 777.6 0 14 12 6 777.6 0 6 13 15 777.6 0 15 14 20 777.6 0 20 15 10 777.6 0 10 16 16 777.6 0 16 17 11 777.6 0 11 18 13 777.6 0 13 19 20 777.6 0 20 20 10 777.6 0 10 21 17 777.6 0 17 22 11 777.6 0 11 23 24 777.6 0 24 24 13 777.6 0 13 25 21 777.6 0 21 26 21 777.6 0 21 27 14 777.6 0 14 28 13 777.6 0 13 29 14 777.6 0 14 30 11 777.6 0 11 31 20 777.6 0 20 32 13 777.6 0 13 33 30 777.6 0 30 34 15 777.6 0 15 35 22 777.6 0 22 36 50 777.6 0 50 37 65 777.6 0 65 38 49 777.6 0 49 39 27 777.6 0 27 40 18 777.6 0 18 41 17 777.6 0 17 42 8 777.6 0 8 43 18 777.6 0 18 44 20 777.6 0 20 45 15 777.6 0 15 46 20 777.6 0 20 47 62 777.6 0 62 48 65 777.6 0 65 49 74 777.6 0 74 50 108 777.6 0 108 51 16 777.6 0 16 52 30 777.6 0 30 53 17 777.6 0 17 54 24 777.6 0 24 55 10 777.6 0 10 56 20 777.6 0 20 57 14 777.6 0 14 58 30 777.6 0 30 59 28 777.6 0 28 60 25 777.6 0 25 61 39 777.6 0 39 62 20 777.6 0 20 63 14 777.6 0 14 64 9 777.6 0 9 65 12 777.6 0 12 66 29 777.6 0 29 67 18 777.6 0 18 68 21 777.6 0 21 69 15 777.6 0 15 70 16 777.6 0 16 71 10 777.6 0 10 72 18 777.6 0 18 73 31 777.6 0 31 74 30 777.6 0 30 75 27 777.6 0 27 76 17 777.6 0 17 77 81 777.6 0 81 78 131 777.6 0 131 79 92 777.6 0 92 80 34 777.6 0 34 81 22 777.6 0 22 82 15 777.6 0 15 83 20 777.6 0 20 84 20 777.6 0 20 85 22 777.6 0 22 86 45 777.6 0 45 87 10 777.6 0 10 88 11 777.6 0 11 89 18 777.6 0 18 90 33 777.6 0 33 91 28 777.6 0 28 92 18 777.6 0 18 93 10 777.6 0 10 94 43 777.6 0 43 95 99 777.6 0 99 96 110 777.6 0 110 97 270 777.6 0 270 98 47 777.6 0 47 99 42 777.6 0 42 100 33 777.6 0 33 101 38 777.6 0 38 102 80 777.6 0 80 103 36 777.6 0 36 104 22 777.6 0 22 105 26 777.6 0 26 106 27 777.6 0 27 107 30 777.6 0 30 108 30 777.6 0 30 109 84 777.6 0 84 110 46 777.6 0 46 111 25 777.6 0 25 112 37 777.6 0 37 113 32 777.6 0 32 114 206 777.6 0 206 115 602 777.6 0 602 116 589 777.6 0 589 117 307 777.6 0 307 118 60 777.6 0 60 119 111 777.6 0 111 120 48 777.6 0 48 121 79 777.6 0 79 122 77 777.6 0 77 123 48 777.6 0 48 124 67 777.6 0 67 125 74 777.6 0 74 126 83 777.6 0 83 127 64 777.6 0 64 128 69 777.6 0 69 129 46 777.6 0 46 130 95 777.6 0 95 131 100 777.6 0 100 132 145 777.6 0 145 133 302 777.6 0 302 134 746 777.6 0 746 135 2383 777.6 0 2383 136 28924 777.6 0 28924 137 7298 777.6 0 7298 138 13167 777.6 0 13167 139 470 777.6 0 470 140 185 777.6 0 185 141 54 777.6 0 54 142 41 777.6 0 41 143 55 777.6 0 55 144 34 777.6 0 34 145 56 777.6 0 56 146 67 777.6 0 67 147 111 777.6 0 111 148 55 777.6 0 55 149 50 777.6 0 50 150 104 777.6 0 104 151 77 777.6 0 77 152 51 777.6 0 51 153 96 777.6 0 96 154 80 777.6 0 80 155 108 777.6 0 108 156 89 777.6 0 89 157 130 777.6 0 130 158 125 777.6 0 125 159 407 777.6 0 407 160 1732 777.6 0 1732 161 1707 777.6 0 1707 162 4696 777.6 0 4696 163 1023 777.6 0 1023 164 51 777.6 0 51 165 44 777.6 0 44 166 63 777.6 0 63 167 64 777.6 0 64 168 55 777.6 0 55 169 52 777.6 0 52 170 145 777.6 0 145 171 29 777.6 0 29 172 40 777.6 0 40 173 56 777.6 0 56 174 111 777.6 0 111 175 192 777.6 0 192 176 113 777.6 0 113 177 99 777.6 0 99 178 173 777.6 0 173 179 62 777.6 0 62 180 90 777.6 0 90 181 160 777.6 0 160 182 169 777.6 0 169 183 371 777.6 0 371 184 200 777.6 0 200 185 268 777.6 0 268 186 313 777.6 0 313 187 495 777.6 0 495 188 573 777.6 0 573 189 677 777.6 0 677 190 682 777.6 0 682 191 1106 777.6 0 1106 192 1492 777.6 0 1492 193 2377 777.6 0 2377 194 3002 777.6 0 3002 195 1210 777.6 0 1210 196 1122 777.6 0 1122 197 2027 777.6 0 2027 198 1594 777.6 0 1594 199 1686 777.6 0 1686 200 2271 777.6 0 2271 201 6325 777.6 0 6325 202 14582 777.6 0 14582 203 15362 777.6 0 15362 204 33780 777.6 0 33780 205 23534 777.6 0 23534 206 20420 777.6 0 20420 207 52614 777.6 0 52614 208 68448 777.6 0 68448 209 89788 777.6 0 89788 210 11477 777.6 0 11477 211 6473 777.6 0 6473 212 8269 777.6 0 8269 213 5080 777.6 0 5080 214 5521 777.6 0 5521 215 1438 777.6 0 1438 216 2003 777.6 0 2003 217 1776 777.6 0 1776 218 785 777.6 0 785 219 1753 777.6 0 1753 220 1441 777.6 0 1441 221 1862 777.6 0 1862 222 7853 777.6 0 7853 223 5343 777.6 0 5343 224 11148 777.6 0 11148 225 1952 777.6 0 1952 226 2610 777.6 0 2610 227 41540 777.6 0 41540 228 43716 777.6 0 43716 229 43414 777.6 0 43414 230 3403 777.6 0 3403 231 42 777.6 0 42 232 20 777.6 0 20 233 21 777.6 0 21 234 38 777.6 0 38 235 17 777.6 0 17 236 21 777.6 0 21 237 421 777.6 0 421 238 374 777.6 0 374 239 262 777.6 0 262 240 4 777.6 0 4 241 3 777.6 0 3 242 5 777.6 0 5 243 6 777.6 0 6 244 12 777.6 0 12 245 56 777.6 0 56 246 54 777.6 0 54 247 88 777.6 0 88 248 87 777.6 0 87 249 8 777.6 0 8 250 4 777.6 0 4 251 2 777.6 0 2 252 9 777.6 0 9 253 18 777.6 0 18 254 29 777.6 0 29 255 31 777.6 0 31 256 161 777.6 0 161 257 294 777.6 0 294 258 508 777.6 0 508 259 556 777.6 0 556 260 368 777.6 0 368 261 1031 777.6 0 1031 262 823 777.6 0 823 263 615 777.6 0 615 264 165 777.6 0 165 265 68 777.6 0 68 266 90 777.6 0 90 267 151 777.6 0 151 268 83 777.6 0 83 269 43 777.6 0 43 270 52 777.6 0 52 271 107 777.6 0 107 272 2069 777.6 0 2069 273 945 777.6 0 945 274 2159 777.6 0 2159 275 51 777.6 0 51 276 33 777.6 0 33 277 145 777.6 0 145 278 236 777.6 0 236 279 749 777.6 0 749 280 83 777.6 0 83 281 44 777.6 0 44 282 19 777.6 0 19 283 24 777.6 0 24 284 52 777.6 0 52 285 47 777.6 0 47 286 429 777.6 0 429 287 567 777.6 0 567 288 342 777.6 0 342 289 97 777.6 0 97 290 41 777.6 0 41 291 26 777.6 0 26 292 162 777.6 0 162 293 363 777.6 0 363 294 311 777.6 0 311 295 10605 777.6 0 10605 296 528 777.6 0 528 297 116 777.6 0 116 298 98 777.6 0 98 299 183 777.6 0 183 300 96 777.6 0 96 301 45 777.6 0 45 Finished in 6.41 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 141,879 Reads with adapters: 41,295 (29.1%) Reads that were too short: 6 (0.0%) Reads written (passing filters): 41,289 (29.1%) Total basepairs processed: 27,026,137 bp Total written (filtered): 11,313,604 bp (41.9%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 41295 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 1 0.0 3 0 0 0 0 1 18 10 0.0 3 0 0 9 1 19 297 0.0 3 0 277 6 10 4 20 40726 0.0 4 40072 621 24 6 3 21 99 0.0 4 11 86 1 1 22 10 0.0 4 0 2 7 0 1 23 140 0.0 4 114 2 0 24 24 4 0.0 4 1 2 0 0 1 25 1 0.0 4 0 0 0 0 1 27 1 0.0 4 1 61 1 0.0 4 0 0 0 0 1 62 1 0.0 4 0 0 0 0 1 64 1 0.0 4 0 0 0 0 1 71 1 0.0 4 0 0 0 0 1 85 1 0.0 4 0 0 0 0 1 132 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 1.73 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 41,289 Reads with adapters: 106 (0.3%) Reads written (passing filters): 41,289 (100.0%) Total basepairs processed: 11,313,604 bp Total written (filtered): 11,311,499 bp (100.0%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 106 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 8.5% C: 1.9% G: 85.8% T: 3.8% 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 6 645.1 0 6 4 2 161.3 0 2 5 2 40.3 0 2 11 84 0.0 1 0 84 12 7 0.0 1 0 7 149 1 0.0 1 1 210 2 0.0 1 1 1 223 1 0.0 1 1 269 1 0.0 1 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.