This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g AATCCT -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 185.82 s (54 us/read; 1.12 M reads/minute). === Summary === Total reads processed: 3,470,393 Reads with adapters: 1,465,948 (42.2%) Reads that were too short: 69,357 (2.0%) Reads written (passing filters): 1,396,591 (40.2%) Total basepairs processed: 1,044,588,293 bp Total written (filtered): 376,611,588 bp (36.1%) === Adapter 1 === Sequence: AATCCT; Type: regular 5'; Length: 6; Trimmed: 1465948 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1198 847.3 0 1198 7 14245 847.3 0 14245 8 757 847.3 0 757 9 14531 847.3 0 14531 10 1025 847.3 0 1025 11 883 847.3 0 883 12 1668 847.3 0 1668 13 4369 847.3 0 4369 14 761 847.3 0 761 15 1594 847.3 0 1594 16 1073 847.3 0 1073 17 1856 847.3 0 1856 18 5641 847.3 0 5641 19 3292 847.3 0 3292 20 2824 847.3 0 2824 21 670 847.3 0 670 22 1202 847.3 0 1202 23 3258 847.3 0 3258 24 3315 847.3 0 3315 25 6318 847.3 0 6318 26 9149 847.3 0 9149 27 9875 847.3 0 9875 28 18561 847.3 0 18561 29 26055 847.3 0 26055 30 260304 847.3 0 260304 31 342884 847.3 0 342884 32 637647 847.3 0 637647 33 2562 847.3 0 2562 34 228 847.3 0 228 35 543 847.3 0 543 36 479 847.3 0 479 37 369 847.3 0 369 38 55 847.3 0 55 39 40 847.3 0 40 40 30 847.3 0 30 41 59 847.3 0 59 42 30 847.3 0 30 43 31 847.3 0 31 44 52 847.3 0 52 45 36 847.3 0 36 46 35 847.3 0 35 47 51 847.3 0 51 48 35 847.3 0 35 49 37 847.3 0 37 50 39 847.3 0 39 51 37 847.3 0 37 52 35 847.3 0 35 53 63 847.3 0 63 54 416 847.3 0 416 55 836 847.3 0 836 56 455 847.3 0 455 57 29 847.3 0 29 58 29 847.3 0 29 59 17 847.3 0 17 60 32 847.3 0 32 61 25 847.3 0 25 62 25 847.3 0 25 63 13 847.3 0 13 64 19 847.3 0 19 65 19 847.3 0 19 66 28 847.3 0 28 67 40 847.3 0 40 68 33 847.3 0 33 69 54 847.3 0 54 70 55 847.3 0 55 71 88 847.3 0 88 72 58 847.3 0 58 73 45 847.3 0 45 74 37 847.3 0 37 75 23 847.3 0 23 76 30 847.3 0 30 77 29 847.3 0 29 78 48 847.3 0 48 79 42 847.3 0 42 80 67 847.3 0 67 81 41 847.3 0 41 82 44 847.3 0 44 83 43 847.3 0 43 84 51 847.3 0 51 85 46 847.3 0 46 86 38 847.3 0 38 87 98 847.3 0 98 88 95 847.3 0 95 89 84 847.3 0 84 90 43 847.3 0 43 91 62 847.3 0 62 92 39 847.3 0 39 93 22 847.3 0 22 94 33 847.3 0 33 95 51 847.3 0 51 96 73 847.3 0 73 97 49 847.3 0 49 98 41 847.3 0 41 99 44 847.3 0 44 100 49 847.3 0 49 101 51 847.3 0 51 102 232 847.3 0 232 103 535 847.3 0 535 104 2581 847.3 0 2581 105 1624 847.3 0 1624 106 585 847.3 0 585 107 244 847.3 0 244 108 33 847.3 0 33 109 46 847.3 0 46 110 45 847.3 0 45 111 57 847.3 0 57 112 62 847.3 0 62 113 50 847.3 0 50 114 54 847.3 0 54 115 32 847.3 0 32 116 66 847.3 0 66 117 39 847.3 0 39 118 64 847.3 0 64 119 41 847.3 0 41 120 57 847.3 0 57 121 50 847.3 0 50 122 64 847.3 0 64 123 117 847.3 0 117 124 375 847.3 0 375 125 252 847.3 0 252 126 160 847.3 0 160 127 69 847.3 0 69 128 44 847.3 0 44 129 42 847.3 0 42 130 45 847.3 0 45 131 40 847.3 0 40 132 37 847.3 0 37 133 48 847.3 0 48 134 49 847.3 0 49 135 58 847.3 0 58 136 62 847.3 0 62 137 398 847.3 0 398 138 201 847.3 0 201 139 187 847.3 0 187 140 66 847.3 0 66 141 71 847.3 0 71 142 123 847.3 0 123 143 106 847.3 0 106 144 63 847.3 0 63 145 40 847.3 0 40 146 57 847.3 0 57 147 68 847.3 0 68 148 67 847.3 0 67 149 88 847.3 0 88 150 73 847.3 0 73 151 84 847.3 0 84 152 35 847.3 0 35 153 44 847.3 0 44 154 44 847.3 0 44 155 73 847.3 0 73 156 29 847.3 0 29 157 60 847.3 0 60 158 76 847.3 0 76 159 175 847.3 0 175 160 85 847.3 0 85 161 354 847.3 0 354 162 57 847.3 0 57 163 73 847.3 0 73 164 86 847.3 0 86 165 58 847.3 0 58 166 87 847.3 0 87 167 66 847.3 0 66 168 76 847.3 0 76 169 51 847.3 0 51 170 61 847.3 0 61 171 66 847.3 0 66 172 43 847.3 0 43 173 53 847.3 0 53 174 47 847.3 0 47 175 49 847.3 0 49 176 47 847.3 0 47 177 55 847.3 0 55 178 42 847.3 0 42 179 52 847.3 0 52 180 42 847.3 0 42 181 49 847.3 0 49 182 70 847.3 0 70 183 88 847.3 0 88 184 99 847.3 0 99 185 85 847.3 0 85 186 100 847.3 0 100 187 72 847.3 0 72 188 64 847.3 0 64 189 123 847.3 0 123 190 57 847.3 0 57 191 38 847.3 0 38 192 39 847.3 0 39 193 38 847.3 0 38 194 48 847.3 0 48 195 40 847.3 0 40 196 52 847.3 0 52 197 34 847.3 0 34 198 56 847.3 0 56 199 68 847.3 0 68 200 66 847.3 0 66 201 78 847.3 0 78 202 60 847.3 0 60 203 43 847.3 0 43 204 113 847.3 0 113 205 423 847.3 0 423 206 381 847.3 0 381 207 144 847.3 0 144 208 47 847.3 0 47 209 48 847.3 0 48 210 57 847.3 0 57 211 50 847.3 0 50 212 83 847.3 0 83 213 75 847.3 0 75 214 69 847.3 0 69 215 72 847.3 0 72 216 66 847.3 0 66 217 94 847.3 0 94 218 79 847.3 0 79 219 74 847.3 0 74 220 79 847.3 0 79 221 55 847.3 0 55 222 47 847.3 0 47 223 60 847.3 0 60 224 57 847.3 0 57 225 76 847.3 0 76 226 114 847.3 0 114 227 117 847.3 0 117 228 114 847.3 0 114 229 74 847.3 0 74 230 82 847.3 0 82 231 145 847.3 0 145 232 144 847.3 0 144 233 98 847.3 0 98 234 67 847.3 0 67 235 39 847.3 0 39 236 68 847.3 0 68 237 77 847.3 0 77 238 54 847.3 0 54 239 84 847.3 0 84 240 122 847.3 0 122 241 104 847.3 0 104 242 101 847.3 0 101 243 110 847.3 0 110 244 139 847.3 0 139 245 161 847.3 0 161 246 229 847.3 0 229 247 383 847.3 0 383 248 136 847.3 0 136 249 203 847.3 0 203 250 291 847.3 0 291 251 254 847.3 0 254 252 252 847.3 0 252 253 474 847.3 0 474 254 3959 847.3 0 3959 255 3106 847.3 0 3106 256 2185 847.3 0 2185 257 712 847.3 0 712 258 777 847.3 0 777 259 1296 847.3 0 1296 260 21247 847.3 0 21247 261 13929 847.3 0 13929 262 7820 847.3 0 7820 263 126 847.3 0 126 264 72 847.3 0 72 265 58 847.3 0 58 266 67 847.3 0 67 267 105 847.3 0 105 268 152 847.3 0 152 269 169 847.3 0 169 270 120 847.3 0 120 271 154 847.3 0 154 272 187 847.3 0 187 273 465 847.3 0 465 274 322 847.3 0 322 275 590 847.3 0 590 276 686 847.3 0 686 277 1171 847.3 0 1171 278 330 847.3 0 330 279 253 847.3 0 253 280 569 847.3 0 569 281 619 847.3 0 619 282 361 847.3 0 361 283 97 847.3 0 97 284 42 847.3 0 42 285 37 847.3 0 37 286 67 847.3 0 67 287 74 847.3 0 74 288 75 847.3 0 75 289 65 847.3 0 65 290 60 847.3 0 60 291 54 847.3 0 54 292 53 847.3 0 53 293 78 847.3 0 78 294 85 847.3 0 85 295 95 847.3 0 95 296 70 847.3 0 70 297 31 847.3 0 31 298 32 847.3 0 32 299 40 847.3 0 40 300 42 847.3 0 42 301 65 847.3 0 65 Finished in 98.48 s (71 us/read; 0.85 M reads/minute). === Summary === Total reads processed: 1,396,591 Reads with adapters: 14,437 (1.0%) Reads that were too short: 57 (0.0%) Reads written (passing filters): 14,380 (1.0%) Total basepairs processed: 376,611,588 bp Total written (filtered): 3,925,294 bp (1.0%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 14437 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 5 0 2 19 154 0.0 3 0 135 17 1 1 20 14036 0.0 4 13547 396 65 18 10 21 38 0.0 4 2 33 3 22 6 0.0 4 3 0 2 1 23 8 0.0 4 1 0 0 7 24 2 0.0 4 0 0 0 0 2 26 1 0.0 4 0 0 0 0 1 31 1 0.0 4 0 0 0 0 1 34 1 0.0 4 0 0 0 0 1 35 1 0.0 4 0 0 0 0 1 41 1 0.0 4 1 45 1 0.0 4 1 49 2 0.0 4 1 0 0 0 1 56 1 0.0 4 1 59 1 0.0 4 0 0 0 0 1 62 1 0.0 4 0 0 0 0 1 71 1 0.0 4 1 72 1 0.0 4 0 0 0 0 1 76 1 0.0 4 0 0 0 0 1 78 1 0.0 4 0 0 0 0 1 79 1 0.0 4 0 0 0 0 1 80 10 0.0 4 0 0 0 0 10 82 1 0.0 4 1 84 29 0.0 4 1 0 0 0 28 87 1 0.0 4 0 0 0 0 1 90 1 0.0 4 0 0 0 0 1 95 1 0.0 4 0 0 0 0 1 97 1 0.0 4 1 98 1 0.0 4 1 101 2 0.0 4 0 0 0 0 2 102 2 0.0 4 0 1 0 0 1 103 1 0.0 4 0 0 0 0 1 107 2 0.0 4 1 0 0 0 1 108 1 0.0 4 0 1 110 1 0.0 4 0 1 112 1 0.0 4 0 0 0 0 1 113 1 0.0 4 1 114 3 0.0 4 0 0 0 0 3 115 1 0.0 4 0 0 0 0 1 116 2 0.0 4 2 119 1 0.0 4 0 1 124 1 0.0 4 1 125 2 0.0 4 0 0 0 0 2 130 7 0.0 4 0 0 0 0 7 135 1 0.0 4 0 1 139 1 0.0 4 1 148 26 0.0 4 0 0 0 0 26 149 15 0.0 4 0 0 0 1 14 150 4 0.0 4 0 0 0 0 4 159 1 0.0 4 0 0 1 160 1 0.0 4 0 0 0 0 1 162 1 0.0 4 0 0 0 0 1 165 1 0.0 4 0 0 0 0 1 166 2 0.0 4 0 0 0 0 2 167 3 0.0 4 0 0 0 0 3 168 2 0.0 4 0 0 0 0 2 171 1 0.0 4 0 0 0 0 1 172 1 0.0 4 1 174 2 0.0 4 1 0 0 1 175 1 0.0 4 0 0 0 0 1 178 1 0.0 4 1 180 1 0.0 4 0 0 0 0 1 181 1 0.0 4 0 0 0 0 1 182 5 0.0 4 0 0 1 0 4 190 1 0.0 4 0 0 0 0 1 193 2 0.0 4 0 1 0 0 1 196 1 0.0 4 0 0 0 0 1 197 2 0.0 4 0 0 0 0 2 203 1 0.0 4 0 1 209 1 0.0 4 0 0 0 0 1 217 1 0.0 4 0 0 0 0 1 218 1 0.0 4 0 0 0 0 1 228 3 0.0 4 0 0 0 0 3 230 1 0.0 4 0 0 0 0 1 231 1 0.0 4 0 0 1 232 1 0.0 4 1 242 1 0.0 4 0 0 0 0 1 245 1 0.0 4 0 0 0 0 1 248 1 0.0 4 0 0 0 0 1 249 1 0.0 4 0 0 0 0 1 251 1 0.0 4 0 0 0 0 1 256 1 0.0 4 0 0 0 0 1 264 1 0.0 4 0 0 0 0 1 265 1 0.0 4 0 0 0 0 1 274 1 0.0 4 0 0 0 0 1 288 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 0.82 s (57 us/read; 1.05 M reads/minute). === Summary === Total reads processed: 14,380 Reads with adapters: 1,040 (7.2%) Reads written (passing filters): 14,380 (100.0%) Total basepairs processed: 3,925,294 bp Total written (filtered): 3,912,304 bp (99.7%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 1040 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 4.6% C: 9.1% G: 84.6% T: 1.6% 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 46 224.7 0 46 4 6 56.2 0 6 9 2 0.1 0 0 2 10 11 0.0 1 1 10 11 870 0.0 1 21 849 12 88 0.0 1 4 84 13 5 0.0 1 0 5 15 2 0.0 1 0 2 135 1 0.0 1 1 152 1 0.0 1 1 210 7 0.0 1 5 2 222 1 0.0 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.