This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AGAAGA -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 58.02 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 2,192,295 Reads with adapters: 472,609 (21.6%) Reads that were too short: 11,677 (0.5%) Reads written (passing filters): 460,932 (21.0%) Total basepairs processed: 659,880,795 bp Total written (filtered): 91,746,513 bp (13.9%) === Adapter 1 === Sequence: AGAAGA; Type: regular 5'; Length: 6; Trimmed: 472609 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 697 535.2 0 697 7 57286 535.2 0 57286 8 65345 535.2 0 65345 9 116 535.2 0 116 10 100 535.2 0 100 11 75 535.2 0 75 12 93 535.2 0 93 13 73 535.2 0 73 14 97 535.2 0 97 15 85 535.2 0 85 16 73 535.2 0 73 17 56 535.2 0 56 18 81 535.2 0 81 19 67 535.2 0 67 20 77 535.2 0 77 21 74 535.2 0 74 22 61 535.2 0 61 23 73 535.2 0 73 24 80 535.2 0 80 25 73 535.2 0 73 26 125 535.2 0 125 27 96 535.2 0 96 28 71 535.2 0 71 29 96 535.2 0 96 30 128 535.2 0 128 31 84 535.2 0 84 32 67 535.2 0 67 33 63 535.2 0 63 34 148 535.2 0 148 35 98 535.2 0 98 36 88 535.2 0 88 37 137 535.2 0 137 38 102 535.2 0 102 39 92 535.2 0 92 40 109 535.2 0 109 41 78 535.2 0 78 42 107 535.2 0 107 43 80 535.2 0 80 44 74 535.2 0 74 45 80 535.2 0 80 46 91 535.2 0 91 47 77 535.2 0 77 48 77 535.2 0 77 49 98 535.2 0 98 50 167 535.2 0 167 51 94 535.2 0 94 52 106 535.2 0 106 53 88 535.2 0 88 54 102 535.2 0 102 55 97 535.2 0 97 56 84 535.2 0 84 57 75 535.2 0 75 58 100 535.2 0 100 59 73 535.2 0 73 60 95 535.2 0 95 61 121 535.2 0 121 62 123 535.2 0 123 63 117 535.2 0 117 64 114 535.2 0 114 65 89 535.2 0 89 66 114 535.2 0 114 67 93 535.2 0 93 68 162 535.2 0 162 69 126 535.2 0 126 70 186 535.2 0 186 71 90 535.2 0 90 72 108 535.2 0 108 73 95 535.2 0 95 74 126 535.2 0 126 75 258 535.2 0 258 76 132 535.2 0 132 77 181 535.2 0 181 78 260 535.2 0 260 79 1677 535.2 0 1677 80 1029 535.2 0 1029 81 1435 535.2 0 1435 82 449 535.2 0 449 83 586 535.2 0 586 84 209 535.2 0 209 85 314 535.2 0 314 86 330 535.2 0 330 87 138 535.2 0 138 88 120 535.2 0 120 89 167 535.2 0 167 90 137 535.2 0 137 91 115 535.2 0 115 92 135 535.2 0 135 93 169 535.2 0 169 94 202 535.2 0 202 95 211 535.2 0 211 96 200 535.2 0 200 97 134 535.2 0 134 98 168 535.2 0 168 99 159 535.2 0 159 100 155 535.2 0 155 101 245 535.2 0 245 102 263 535.2 0 263 103 261 535.2 0 261 104 307 535.2 0 307 105 576 535.2 0 576 106 262 535.2 0 262 107 315 535.2 0 315 108 559 535.2 0 559 109 303 535.2 0 303 110 330 535.2 0 330 111 558 535.2 0 558 112 476 535.2 0 476 113 465 535.2 0 465 114 429 535.2 0 429 115 704 535.2 0 704 116 765 535.2 0 765 117 1148 535.2 0 1148 118 15123 535.2 0 15123 119 23528 535.2 0 23528 120 22022 535.2 0 22022 121 4628 535.2 0 4628 122 4930 535.2 0 4930 123 2827 535.2 0 2827 124 658 535.2 0 658 125 434 535.2 0 434 126 614 535.2 0 614 127 535 535.2 0 535 128 428 535.2 0 428 129 422 535.2 0 422 130 519 535.2 0 519 131 778 535.2 0 778 132 1221 535.2 0 1221 133 758 535.2 0 758 134 751 535.2 0 751 135 1061 535.2 0 1061 136 747 535.2 0 747 137 1084 535.2 0 1084 138 1505 535.2 0 1505 139 3892 535.2 0 3892 140 8527 535.2 0 8527 141 30793 535.2 0 30793 142 16826 535.2 0 16826 143 2131 535.2 0 2131 144 2423 535.2 0 2423 145 23090 535.2 0 23090 146 47622 535.2 0 47622 147 52060 535.2 0 52060 148 8865 535.2 0 8865 149 3196 535.2 0 3196 150 540 535.2 0 540 151 428 535.2 0 428 152 463 535.2 0 463 153 326 535.2 0 326 154 376 535.2 0 376 155 535 535.2 0 535 156 290 535.2 0 290 157 348 535.2 0 348 158 694 535.2 0 694 159 750 535.2 0 750 160 2210 535.2 0 2210 161 375 535.2 0 375 162 371 535.2 0 371 163 398 535.2 0 398 164 561 535.2 0 561 165 4665 535.2 0 4665 166 7999 535.2 0 7999 167 4364 535.2 0 4364 168 297 535.2 0 297 169 155 535.2 0 155 170 103 535.2 0 103 171 115 535.2 0 115 172 123 535.2 0 123 173 115 535.2 0 115 174 137 535.2 0 137 175 146 535.2 0 146 176 113 535.2 0 113 177 123 535.2 0 123 178 111 535.2 0 111 179 116 535.2 0 116 180 109 535.2 0 109 181 128 535.2 0 128 182 144 535.2 0 144 183 133 535.2 0 133 184 120 535.2 0 120 185 122 535.2 0 122 186 121 535.2 0 121 187 91 535.2 0 91 188 119 535.2 0 119 189 102 535.2 0 102 190 109 535.2 0 109 191 107 535.2 0 107 192 123 535.2 0 123 193 153 535.2 0 153 194 200 535.2 0 200 195 124 535.2 0 124 196 121 535.2 0 121 197 147 535.2 0 147 198 112 535.2 0 112 199 114 535.2 0 114 200 175 535.2 0 175 201 184 535.2 0 184 202 113 535.2 0 113 203 107 535.2 0 107 204 145 535.2 0 145 205 133 535.2 0 133 206 128 535.2 0 128 207 128 535.2 0 128 208 135 535.2 0 135 209 138 535.2 0 138 210 131 535.2 0 131 211 114 535.2 0 114 212 104 535.2 0 104 213 95 535.2 0 95 214 111 535.2 0 111 215 115 535.2 0 115 216 264 535.2 0 264 217 413 535.2 0 413 218 327 535.2 0 327 219 269 535.2 0 269 220 100 535.2 0 100 221 141 535.2 0 141 222 90 535.2 0 90 223 97 535.2 0 97 224 99 535.2 0 99 225 119 535.2 0 119 226 143 535.2 0 143 227 95 535.2 0 95 228 82 535.2 0 82 229 80 535.2 0 80 230 128 535.2 0 128 231 102 535.2 0 102 232 74 535.2 0 74 233 93 535.2 0 93 234 111 535.2 0 111 235 90 535.2 0 90 236 101 535.2 0 101 237 99 535.2 0 99 238 98 535.2 0 98 239 106 535.2 0 106 240 96 535.2 0 96 241 118 535.2 0 118 242 93 535.2 0 93 243 90 535.2 0 90 244 97 535.2 0 97 245 88 535.2 0 88 246 133 535.2 0 133 247 108 535.2 0 108 248 115 535.2 0 115 249 86 535.2 0 86 250 79 535.2 0 79 251 72 535.2 0 72 252 81 535.2 0 81 253 91 535.2 0 91 254 98 535.2 0 98 255 122 535.2 0 122 256 115 535.2 0 115 257 113 535.2 0 113 258 105 535.2 0 105 259 97 535.2 0 97 260 93 535.2 0 93 261 121 535.2 0 121 262 130 535.2 0 130 263 112 535.2 0 112 264 92 535.2 0 92 265 118 535.2 0 118 266 117 535.2 0 117 267 118 535.2 0 118 268 78 535.2 0 78 269 109 535.2 0 109 270 97 535.2 0 97 271 116 535.2 0 116 272 85 535.2 0 85 273 93 535.2 0 93 274 103 535.2 0 103 275 104 535.2 0 104 276 96 535.2 0 96 277 91 535.2 0 91 278 110 535.2 0 110 279 92 535.2 0 92 280 89 535.2 0 89 281 114 535.2 0 114 282 103 535.2 0 103 283 88 535.2 0 88 284 107 535.2 0 107 285 105 535.2 0 105 286 93 535.2 0 93 287 104 535.2 0 104 288 132 535.2 0 132 289 97 535.2 0 97 290 104 535.2 0 104 291 116 535.2 0 116 292 109 535.2 0 109 293 119 535.2 0 119 294 130 535.2 0 130 295 112 535.2 0 112 296 106 535.2 0 106 297 132 535.2 0 132 298 100 535.2 0 100 299 105 535.2 0 105 300 126 535.2 0 126 301 296 535.2 0 296 Finished in 18.37 s (40 us/read; 1.51 M reads/minute). === Summary === Total reads processed: 460,932 Reads with adapters: 67,944 (14.7%) Reads that were too short: 60 (0.0%) Reads written (passing filters): 67,884 (14.7%) Total basepairs processed: 91,746,513 bp Total written (filtered): 18,353,590 bp (20.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 67944 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 4 0.0 3 0 0 0 3 1 18 19 0.0 3 0 0 17 2 19 615 0.0 3 0 610 3 2 20 65302 0.0 4 64353 917 25 5 2 21 183 0.0 4 27 151 5 22 20 0.0 4 3 0 15 2 23 39 0.0 4 6 0 0 30 3 24 6 0.0 4 0 0 0 0 6 25 2 0.0 4 0 0 0 0 2 26 2 0.0 4 1 0 0 0 1 32 1 0.0 4 0 1 36 1 0.0 4 0 0 0 0 1 37 1 0.0 4 1 41 5 0.0 4 0 0 0 0 5 42 3 0.0 4 0 0 0 0 3 43 1 0.0 4 1 48 2 0.0 4 0 0 0 0 2 49 1 0.0 4 0 0 0 0 1 50 2 0.0 4 0 0 0 0 2 53 7 0.0 4 0 0 0 0 7 57 1 0.0 4 1 73 1 0.0 4 0 0 0 0 1 76 2 0.0 4 0 0 0 0 2 77 1 0.0 4 0 0 0 0 1 79 2 0.0 4 1 0 0 0 1 84 1 0.0 4 0 0 0 0 1 87 1 0.0 4 0 0 0 0 1 91 1 0.0 4 0 0 0 0 1 96 1 0.0 4 0 0 0 0 1 99 1 0.0 4 0 0 0 0 1 100 2 0.0 4 0 0 0 0 2 101 1 0.0 4 0 0 0 0 1 102 2 0.0 4 0 0 0 0 2 107 1 0.0 4 0 0 0 0 1 114 1 0.0 4 0 1 116 1 0.0 4 0 0 0 0 1 122 1 0.0 4 0 0 0 0 1 124 3 0.0 4 0 0 0 0 3 125 5 0.0 4 0 0 0 0 5 126 29 0.0 4 0 0 0 0 29 127 1623 0.0 4 0 0 0 0 1623 128 2 0.0 4 0 0 0 0 2 129 11 0.0 4 0 0 0 0 11 143 2 0.0 4 0 0 0 0 2 144 3 0.0 4 0 0 0 0 3 146 2 0.0 4 0 0 0 0 2 155 3 0.0 4 0 0 0 0 3 161 1 0.0 4 0 0 0 0 1 172 2 0.0 4 0 0 0 0 2 177 2 0.0 4 0 0 0 0 2 179 1 0.0 4 0 0 0 0 1 180 2 0.0 4 1 0 0 0 1 181 2 0.0 4 0 0 0 0 2 192 1 0.0 4 0 0 0 0 1 204 1 0.0 4 0 0 0 0 1 212 1 0.0 4 0 0 0 0 1 220 1 0.0 4 0 0 0 0 1 228 3 0.0 4 0 0 0 0 3 235 1 0.0 4 0 0 0 0 1 251 1 0.0 4 0 0 0 0 1 281 1 0.0 4 0 0 0 0 1 282 1 0.0 4 0 0 0 0 1 283 1 0.0 4 0 0 0 0 1 288 1 0.0 4 0 0 0 0 1 291 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 2.36 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 67,884 Reads with adapters: 7,790 (11.5%) Reads written (passing filters): 67,884 (100.0%) Total basepairs processed: 18,353,590 bp Total written (filtered): 18,266,747 bp (99.5%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 7790 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 1.1% C: 2.7% G: 95.0% T: 1.2% 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 38 1060.7 0 38 4 305 265.2 0 305 5 7 66.3 0 7 6 95 16.6 0 95 7 3 4.1 0 3 8 1 1.0 0 1 9 144 0.3 0 2 142 10 1396 0.1 1 41 1355 11 5751 0.0 1 24 5727 12 9 0.0 1 0 9 13 1 0.0 1 0 1 69 1 0.0 1 1 134 1 0.0 1 1 144 1 0.0 1 1 151 29 0.0 1 1 28 152 1 0.0 1 0 1 170 2 0.0 1 2 171 1 0.0 1 1 209 3 0.0 1 3 221 1 0.0 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.