This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g CGGCCA -e 0 -O 6 - Trimming 1 adapter with at most 0.0% errors in single-end mode ... Finished in 69.23 s (26 us/read; 2.28 M reads/minute). === Summary === Total reads processed: 2,630,299 Reads with adapters: 93,465 (3.6%) Reads that were too short: 30,976 (1.2%) Reads written (passing filters): 62,489 (2.4%) Total basepairs processed: 791,719,999 bp Total written (filtered): 14,739,146 bp (1.9%) === Adapter 1 === Sequence: CGGCCA; Type: regular 5'; Length: 6; Trimmed: 93465 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1758 642.2 0 1758 7 16261 642.2 0 16261 8 748 642.2 0 748 9 15437 642.2 0 15437 10 51 642.2 0 51 11 294 642.2 0 294 12 37 642.2 0 37 13 38 642.2 0 38 14 37 642.2 0 37 15 36 642.2 0 36 16 24 642.2 0 24 17 38 642.2 0 38 18 49 642.2 0 49 19 48 642.2 0 48 20 47 642.2 0 47 21 53 642.2 0 53 22 42 642.2 0 42 23 34 642.2 0 34 24 46 642.2 0 46 25 41 642.2 0 41 26 55 642.2 0 55 27 45 642.2 0 45 28 43 642.2 0 43 29 45 642.2 0 45 30 56 642.2 0 56 31 58 642.2 0 58 32 39 642.2 0 39 33 43 642.2 0 43 34 54 642.2 0 54 35 52 642.2 0 52 36 47 642.2 0 47 37 55 642.2 0 55 38 72 642.2 0 72 39 45 642.2 0 45 40 37 642.2 0 37 41 59 642.2 0 59 42 99 642.2 0 99 43 94 642.2 0 94 44 43 642.2 0 43 45 36 642.2 0 36 46 69 642.2 0 69 47 61 642.2 0 61 48 59 642.2 0 59 49 67 642.2 0 67 50 45 642.2 0 45 51 43 642.2 0 43 52 66 642.2 0 66 53 51 642.2 0 51 54 81 642.2 0 81 55 66 642.2 0 66 56 56 642.2 0 56 57 58 642.2 0 58 58 59 642.2 0 59 59 71 642.2 0 71 60 56 642.2 0 56 61 39 642.2 0 39 62 37 642.2 0 37 63 35 642.2 0 35 64 154 642.2 0 154 65 214 642.2 0 214 66 163 642.2 0 163 67 61 642.2 0 61 68 51 642.2 0 51 69 48 642.2 0 48 70 63 642.2 0 63 71 66 642.2 0 66 72 74 642.2 0 74 73 132 642.2 0 132 74 738 642.2 0 738 75 254 642.2 0 254 76 165 642.2 0 165 77 78 642.2 0 78 78 82 642.2 0 82 79 55 642.2 0 55 80 66 642.2 0 66 81 77 642.2 0 77 82 52 642.2 0 52 83 88 642.2 0 88 84 48 642.2 0 48 85 50 642.2 0 50 86 58 642.2 0 58 87 104 642.2 0 104 88 81 642.2 0 81 89 215 642.2 0 215 90 57 642.2 0 57 91 37 642.2 0 37 92 108 642.2 0 108 93 64 642.2 0 64 94 47 642.2 0 47 95 67 642.2 0 67 96 68 642.2 0 68 97 68 642.2 0 68 98 72 642.2 0 72 99 74 642.2 0 74 100 82 642.2 0 82 101 121 642.2 0 121 102 61 642.2 0 61 103 47 642.2 0 47 104 88 642.2 0 88 105 63 642.2 0 63 106 53 642.2 0 53 107 44 642.2 0 44 108 60 642.2 0 60 109 78 642.2 0 78 110 47 642.2 0 47 111 73 642.2 0 73 112 70 642.2 0 70 113 68 642.2 0 68 114 168 642.2 0 168 115 72 642.2 0 72 116 67 642.2 0 67 117 45 642.2 0 45 118 79 642.2 0 79 119 53 642.2 0 53 120 58 642.2 0 58 121 63 642.2 0 63 122 55 642.2 0 55 123 63 642.2 0 63 124 59 642.2 0 59 125 65 642.2 0 65 126 51 642.2 0 51 127 59 642.2 0 59 128 55 642.2 0 55 129 52 642.2 0 52 130 56 642.2 0 56 131 62 642.2 0 62 132 66 642.2 0 66 133 91 642.2 0 91 134 46 642.2 0 46 135 61 642.2 0 61 136 52 642.2 0 52 137 75 642.2 0 75 138 88 642.2 0 88 139 76 642.2 0 76 140 50 642.2 0 50 141 58 642.2 0 58 142 49 642.2 0 49 143 168 642.2 0 168 144 71 642.2 0 71 145 81 642.2 0 81 146 74 642.2 0 74 147 55 642.2 0 55 148 77 642.2 0 77 149 64 642.2 0 64 150 103 642.2 0 103 151 268 642.2 0 268 152 256 642.2 0 256 153 400 642.2 0 400 154 200 642.2 0 200 155 333 642.2 0 333 156 3754 642.2 0 3754 157 1087 642.2 0 1087 158 3323 642.2 0 3323 159 299 642.2 0 299 160 83 642.2 0 83 161 230 642.2 0 230 162 83 642.2 0 83 163 329 642.2 0 329 164 134 642.2 0 134 165 239 642.2 0 239 166 246 642.2 0 246 167 110 642.2 0 110 168 43 642.2 0 43 169 75 642.2 0 75 170 141 642.2 0 141 171 2027 642.2 0 2027 172 164 642.2 0 164 173 140 642.2 0 140 174 65 642.2 0 65 175 82 642.2 0 82 176 354 642.2 0 354 177 657 642.2 0 657 178 588 642.2 0 588 179 285 642.2 0 285 180 52 642.2 0 52 181 63 642.2 0 63 182 106 642.2 0 106 183 154 642.2 0 154 184 74 642.2 0 74 185 61 642.2 0 61 186 56 642.2 0 56 187 66 642.2 0 66 188 185 642.2 0 185 189 116 642.2 0 116 190 72 642.2 0 72 191 172 642.2 0 172 192 72 642.2 0 72 193 51 642.2 0 51 194 47 642.2 0 47 195 49 642.2 0 49 196 60 642.2 0 60 197 62 642.2 0 62 198 53 642.2 0 53 199 79 642.2 0 79 200 77 642.2 0 77 201 111 642.2 0 111 202 93 642.2 0 93 203 64 642.2 0 64 204 38 642.2 0 38 205 65 642.2 0 65 206 69 642.2 0 69 207 74 642.2 0 74 208 83 642.2 0 83 209 55 642.2 0 55 210 52 642.2 0 52 211 58 642.2 0 58 212 44 642.2 0 44 213 55 642.2 0 55 214 73 642.2 0 73 215 151 642.2 0 151 216 87 642.2 0 87 217 66 642.2 0 66 218 35 642.2 0 35 219 47 642.2 0 47 220 74 642.2 0 74 221 60 642.2 0 60 222 59 642.2 0 59 223 85 642.2 0 85 224 70 642.2 0 70 225 44 642.2 0 44 226 65 642.2 0 65 227 59 642.2 0 59 228 102 642.2 0 102 229 123 642.2 0 123 230 87 642.2 0 87 231 67 642.2 0 67 232 93 642.2 0 93 233 573 642.2 0 573 234 283 642.2 0 283 235 160 642.2 0 160 236 49 642.2 0 49 237 275 642.2 0 275 238 157 642.2 0 157 239 88 642.2 0 88 240 132 642.2 0 132 241 66 642.2 0 66 242 63 642.2 0 63 243 76 642.2 0 76 244 91 642.2 0 91 245 79 642.2 0 79 246 70 642.2 0 70 247 71 642.2 0 71 248 116 642.2 0 116 249 225 642.2 0 225 250 217 642.2 0 217 251 175 642.2 0 175 252 134 642.2 0 134 253 1109 642.2 0 1109 254 448 642.2 0 448 255 962 642.2 0 962 256 89 642.2 0 89 257 121 642.2 0 121 258 113 642.2 0 113 259 649 642.2 0 649 260 315 642.2 0 315 261 1622 642.2 0 1622 262 3365 642.2 0 3365 263 4174 642.2 0 4174 264 2563 642.2 0 2563 265 1219 642.2 0 1219 266 50 642.2 0 50 267 69 642.2 0 69 268 71 642.2 0 71 269 63 642.2 0 63 270 58 642.2 0 58 271 45 642.2 0 45 272 59 642.2 0 59 273 59 642.2 0 59 274 58 642.2 0 58 275 57 642.2 0 57 276 66 642.2 0 66 277 140 642.2 0 140 278 141 642.2 0 141 279 93 642.2 0 93 280 74 642.2 0 74 281 56 642.2 0 56 282 181 642.2 0 181 283 105 642.2 0 105 284 129 642.2 0 129 285 126 642.2 0 126 286 69 642.2 0 69 287 242 642.2 0 242 288 436 642.2 0 436 289 308 642.2 0 308 290 80 642.2 0 80 291 102 642.2 0 102 292 211 642.2 0 211 293 171 642.2 0 171 294 117 642.2 0 117 295 164 642.2 0 164 296 178 642.2 0 178 297 218 642.2 0 218 298 1477 642.2 0 1477 299 1396 642.2 0 1396 300 1977 642.2 0 1977 301 84 642.2 0 84 Finished in 2.73 s (44 us/read; 1.37 M reads/minute). === Summary === Total reads processed: 62,489 Reads with adapters: 16,526 (26.4%) Reads that were too short: 30 (0.0%) Reads written (passing filters): 16,496 (26.4%) Total basepairs processed: 14,739,146 bp Total written (filtered): 4,516,237 bp (30.6%) === Adapter 1 === Sequence: CCTAYGGGRBGCASCAG; Type: regular 5'; Length: 17; Trimmed: 16526 times. No. of allowed errors: 0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-17 bp: 3 Overview of removed sequences length count expect max.err error counts 15 98 0.0 3 0 0 3 95 16 69 0.0 3 0 67 2 17 16224 0.0 3 15952 268 2 2 18 56 0.0 3 4 39 1 12 19 8 0.0 3 0 0 8 20 5 0.0 3 0 0 0 5 21 2 0.0 3 2 26 1 0.0 3 1 29 5 0.0 3 0 0 0 5 30 1 0.0 3 1 37 1 0.0 3 0 0 0 1 41 7 0.0 3 0 0 0 7 42 1 0.0 3 0 0 0 1 43 2 0.0 3 0 0 0 2 66 2 0.0 3 0 0 0 2 78 1 0.0 3 0 0 0 1 83 3 0.0 3 0 0 0 3 85 1 0.0 3 0 0 0 1 93 1 0.0 3 0 0 0 1 94 2 0.0 3 0 0 1 1 101 1 0.0 3 1 105 1 0.0 3 0 0 0 1 108 1 0.0 3 0 0 1 122 1 0.0 3 0 0 0 1 127 4 0.0 3 0 0 0 4 130 3 0.0 3 0 0 0 3 136 1 0.0 3 0 0 0 1 140 1 0.0 3 0 0 0 1 142 1 0.0 3 0 0 0 1 145 3 0.0 3 0 0 1 2 148 1 0.0 3 0 0 0 1 151 3 0.0 3 0 0 0 3 153 1 0.0 3 0 0 0 1 154 1 0.0 3 0 0 0 1 164 1 0.0 3 0 0 0 1 165 1 0.0 3 0 0 0 1 179 1 0.0 3 0 0 0 1 188 1 0.0 3 0 0 0 1 194 1 0.0 3 0 0 0 1 195 2 0.0 3 0 0 0 2 196 1 0.0 3 0 0 0 1 205 1 0.0 3 0 0 0 1 217 1 0.0 3 0 0 0 1 277 1 0.0 3 0 0 0 1 282 2 0.0 3 0 0 0 2 This is cutadapt 1.11 with Python 2.7.12 Command line parameters: -a taatctatgggnncatcagg - Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.58 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 16,496 Reads with adapters: 1,156 (7.0%) Reads written (passing filters): 16,496 (100.0%) Total basepairs processed: 4,516,237 bp Total written (filtered): 4,512,707 bp (99.9%) === Adapter 1 === Sequence: TAATCTATGGGNNCATCAGG; Type: regular 3'; Length: 20; Trimmed: 1156 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20 bp: 2 Bases preceding removed adapters: A: 87.1% C: 7.8% G: 3.7% T: 1.4% 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 3 1095 257.8 0 1095 4 60 64.4 0 60 5 1 16.1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.