This is cutadapt 1.11 with Python 2.7.12 Command line parameters: --discard-untrimmed --minimum-length 100 -g TCCAGC -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 184.15 s (51 us/read; 1.18 M reads/minute). === Summary === Total reads processed: 3,634,272 Reads with adapters: 671,619 (18.5%) Reads that were too short: 13,941 (0.4%) Reads written (passing filters): 657,678 (18.1%) Total basepairs processed: 1,093,915,872 bp Total written (filtered): 143,791,083 bp (13.1%) === Adapter 1 === Sequence: TCCAGC; Type: regular 5'; Length: 6; Trimmed: 671619 times. No. of allowed errors: 0-6 bp: 0 Overview of removed sequences length count expect max.err error counts 6 710 887.3 0 710 7 1260 887.3 0 1260 8 25827 887.3 0 25827 9 29421 887.3 0 29421 10 107 887.3 0 107 11 145 887.3 0 145 12 129 887.3 0 129 13 120 887.3 0 120 14 57 887.3 0 57 15 96 887.3 0 96 16 76 887.3 0 76 17 81 887.3 0 81 18 169 887.3 0 169 19 169 887.3 0 169 20 158 887.3 0 158 21 111 887.3 0 111 22 166 887.3 0 166 23 139 887.3 0 139 24 135 887.3 0 135 25 87 887.3 0 87 26 74 887.3 0 74 27 86 887.3 0 86 28 115 887.3 0 115 29 359 887.3 0 359 30 150 887.3 0 150 31 93 887.3 0 93 32 124 887.3 0 124 33 79 887.3 0 79 34 79 887.3 0 79 35 119 887.3 0 119 36 258 887.3 0 258 37 212 887.3 0 212 38 532 887.3 0 532 39 220 887.3 0 220 40 127 887.3 0 127 41 90 887.3 0 90 42 158 887.3 0 158 43 132 887.3 0 132 44 184 887.3 0 184 45 206 887.3 0 206 46 257 887.3 0 257 47 330 887.3 0 330 48 625 887.3 0 625 49 1970 887.3 0 1970 50 418 887.3 0 418 51 552 887.3 0 552 52 1153 887.3 0 1153 53 560 887.3 0 560 54 654 887.3 0 654 55 1174 887.3 0 1174 56 1302 887.3 0 1302 57 1399 887.3 0 1399 58 1354 887.3 0 1354 59 2951 887.3 0 2951 60 3761 887.3 0 3761 61 8052 887.3 0 8052 62 148453 887.3 0 148453 63 139156 887.3 0 139156 64 92882 887.3 0 92882 65 1173 887.3 0 1173 66 93 887.3 0 93 67 78 887.3 0 78 68 73 887.3 0 73 69 98 887.3 0 98 70 155 887.3 0 155 71 656 887.3 0 656 72 660 887.3 0 660 73 630 887.3 0 630 74 240 887.3 0 240 75 273 887.3 0 273 76 3550 887.3 0 3550 77 6951 887.3 0 6951 78 6115 887.3 0 6115 79 389 887.3 0 389 80 82 887.3 0 82 81 48 887.3 0 48 82 78 887.3 0 78 83 79 887.3 0 79 84 68 887.3 0 68 85 79 887.3 0 79 86 77 887.3 0 77 87 72 887.3 0 72 88 62 887.3 0 62 89 67 887.3 0 67 90 79 887.3 0 79 91 62 887.3 0 62 92 59 887.3 0 59 93 78 887.3 0 78 94 84 887.3 0 84 95 69 887.3 0 69 96 64 887.3 0 64 97 36 887.3 0 36 98 90 887.3 0 90 99 401 887.3 0 401 100 72 887.3 0 72 101 54 887.3 0 54 102 81 887.3 0 81 103 96 887.3 0 96 104 162 887.3 0 162 105 121 887.3 0 121 106 106 887.3 0 106 107 279 887.3 0 279 108 393 887.3 0 393 109 404 887.3 0 404 110 139 887.3 0 139 111 112 887.3 0 112 112 99 887.3 0 99 113 86 887.3 0 86 114 55 887.3 0 55 115 117 887.3 0 117 116 65 887.3 0 65 117 107 887.3 0 107 118 96 887.3 0 96 119 67 887.3 0 67 120 95 887.3 0 95 121 86 887.3 0 86 122 69 887.3 0 69 123 63 887.3 0 63 124 78 887.3 0 78 125 123 887.3 0 123 126 210 887.3 0 210 127 304 887.3 0 304 128 174 887.3 0 174 129 192 887.3 0 192 130 109 887.3 0 109 131 86 887.3 0 86 132 114 887.3 0 114 133 85 887.3 0 85 134 94 887.3 0 94 135 90 887.3 0 90 136 86 887.3 0 86 137 299 887.3 0 299 138 130 887.3 0 130 139 175 887.3 0 175 140 264 887.3 0 264 141 247 887.3 0 247 142 434 887.3 0 434 143 621 887.3 0 621 144 9744 887.3 0 9744 145 12851 887.3 0 12851 146 9912 887.3 0 9912 147 511 887.3 0 511 148 123 887.3 0 123 149 141 887.3 0 141 150 107 887.3 0 107 151 131 887.3 0 131 152 172 887.3 0 172 153 151 887.3 0 151 154 170 887.3 0 170 155 215 887.3 0 215 156 1866 887.3 0 1866 157 2536 887.3 0 2536 158 2156 887.3 0 2156 159 321 887.3 0 321 160 350 887.3 0 350 161 489 887.3 0 489 162 1357 887.3 0 1357 163 2454 887.3 0 2454 164 54299 887.3 0 54299 165 26728 887.3 0 26728 166 23409 887.3 0 23409 167 290 887.3 0 290 168 271 887.3 0 271 169 502 887.3 0 502 170 529 887.3 0 529 171 1040 887.3 0 1040 172 286 887.3 0 286 173 272 887.3 0 272 174 228 887.3 0 228 175 87 887.3 0 87 176 64 887.3 0 64 177 54 887.3 0 54 178 94 887.3 0 94 179 207 887.3 0 207 180 312 887.3 0 312 181 283 887.3 0 283 182 78 887.3 0 78 183 104 887.3 0 104 184 145 887.3 0 145 185 168 887.3 0 168 186 132 887.3 0 132 187 92 887.3 0 92 188 97 887.3 0 97 189 275 887.3 0 275 190 814 887.3 0 814 191 651 887.3 0 651 192 318 887.3 0 318 193 72 887.3 0 72 194 73 887.3 0 73 195 70 887.3 0 70 196 88 887.3 0 88 197 85 887.3 0 85 198 97 887.3 0 97 199 81 887.3 0 81 200 82 887.3 0 82 201 74 887.3 0 74 202 77 887.3 0 77 203 84 887.3 0 84 204 80 887.3 0 80 205 77 887.3 0 77 206 76 887.3 0 76 207 74 887.3 0 74 208 85 887.3 0 85 209 64 887.3 0 64 210 58 887.3 0 58 211 59 887.3 0 59 212 78 887.3 0 78 213 95 887.3 0 95 214 111 887.3 0 111 215 108 887.3 0 108 216 138 887.3 0 138 217 191 887.3 0 191 218 138 887.3 0 138 219 107 887.3 0 107 220 63 887.3 0 63 221 47 887.3 0 47 222 68 887.3 0 68 223 87 887.3 0 87 224 95 887.3 0 95 225 107 887.3 0 107 226 479 887.3 0 479 227 189 887.3 0 189 228 145 887.3 0 145 229 644 887.3 0 644 230 470 887.3 0 470 231 1655 887.3 0 1655 232 84 887.3 0 84 233 70 887.3 0 70 234 54 887.3 0 54 235 64 887.3 0 64 236 123 887.3 0 123 237 120 887.3 0 120 238 127 887.3 0 127 239 113 887.3 0 113 240 90 887.3 0 90 241 110 887.3 0 110 242 60 887.3 0 60 243 84 887.3 0 84 244 67 887.3 0 67 245 84 887.3 0 84 246 72 887.3 0 72 247 75 887.3 0 75 248 97 887.3 0 97 249 75 887.3 0 75 250 74 887.3 0 74 251 81 887.3 0 81 252 82 887.3 0 82 253 57 887.3 0 57 254 81 887.3 0 81 255 79 887.3 0 79 256 84 887.3 0 84 257 67 887.3 0 67 258 54 887.3 0 54 259 84 887.3 0 84 260 141 887.3 0 141 261 155 887.3 0 155 262 199 887.3 0 199 263 115 887.3 0 115 264 77 887.3 0 77 265 99 887.3 0 99 266 92 887.3 0 92 267 117 887.3 0 117 268 98 887.3 0 98 269 66 887.3 0 66 270 78 887.3 0 78 271 96 887.3 0 96 272 99 887.3 0 99 273 96 887.3 0 96 274 98 887.3 0 98 275 79 887.3 0 79 276 82 887.3 0 82 277 288 887.3 0 288 278 113 887.3 0 113 279 193 887.3 0 193 280 87 887.3 0 87 281 257 887.3 0 257 282 69 887.3 0 69 283 82 887.3 0 82 284 74 887.3 0 74 285 127 887.3 0 127 286 183 887.3 0 183 287 409 887.3 0 409 288 531 887.3 0 531 289 329 887.3 0 329 290 136 887.3 0 136 291 87 887.3 0 87 292 98 887.3 0 98 293 83 887.3 0 83 294 98 887.3 0 98 295 105 887.3 0 105 296 250 887.3 0 250 297 156 887.3 0 156 298 88 887.3 0 88 299 72 887.3 0 72 300 84 887.3 0 84 301 94 887.3 0 94 Finished in 44.54 s (68 us/read; 0.89 M reads/minute). === Summary === Total reads processed: 657,678 Reads with adapters: 63,064 (9.6%) Reads that were too short: 190 (0.0%) Reads written (passing filters): 62,874 (9.6%) Total basepairs processed: 143,791,083 bp Total written (filtered): 13,799,738 bp (9.6%) === Adapter 1 === Sequence: GGACTACNNGGGTATCTAAT; Type: regular 5'; Length: 20; Trimmed: 63064 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 9 0.0 3 0 0 9 19 345 0.0 3 0 341 3 1 20 31077 0.0 4 30534 521 20 1 1 21 64 0.0 4 10 50 4 22 6 0.0 4 2 1 3 23 18 0.0 4 0 0 0 17 1 24 1 0.0 4 0 0 0 0 1 25 1 0.0 4 0 0 0 0 1 27 1 0.0 4 0 0 0 0 1 34 80 0.0 4 0 0 0 0 80 37 3 0.0 4 0 0 0 0 3 43 1 0.0 4 0 0 0 0 1 51 1 0.0 4 0 0 0 0 1 52 2 0.0 4 0 0 0 0 2 65 1 0.0 4 0 0 0 0 1 67 1 0.0 4 0 0 0 0 1 69 4 0.0 4 0 0 0 0 4 70 37 0.0 4 0 0 0 0 37 71 25 0.0 4 0 0 0 0 25 72 30754 0.0 4 0 0 0 0 30754 74 6 0.0 4 0 0 0 0 6 75 20 0.0 4 0 0 0 0 20 77 1 0.0 4 1 79 1 0.0 4 0 0 0 0 1 80 2 0.0 4 0 0 0 0 2 85 1 0.0 4 1 90 1 0.0 4 1 98 2 0.0 4 0 0 0 0 2 102 1 0.0 4 1 110 1 0.0 4 0 0 0 0 1 112 3 0.0 4 0 0 0 0 3 121 1 0.0 4 0 0 0 0 1 125 2 0.0 4 0 0 0 0 2 126 4 0.0 4 0 0 0 0 4 127 401 0.0 4 0 0 0 0 401 128 1 0.0 4 0 0 0 0 1 129 1 0.0 4 0 0 0 0 1 135 1 0.0 4 0 1 147 2 0.0 4 0 0 0 0 2 153 1 0.0 4 0 0 0 0 1 155 1 0.0 4 0 0 0 0 1 157 1 0.0 4 0 0 0 0 1 160 2 0.0 4 2 166 1 0.0 4 0 0 0 0 1 168 1 0.0 4 0 0 0 0 1 169 1 0.0 4 0 0 0 0 1 170 3 0.0 4 0 0 0 0 3 173 68 0.0 4 0 0 0 0 68 174 25 0.0 4 0 0 0 2 23 175 2 0.0 4 0 0 0 0 2 177 2 0.0 4 1 0 0 0 1 178 1 0.0 4 0 0 0 0 1 179 7 0.0 4 0 0 0 0 7 180 4 0.0 4 0 0 0 0 4 181 10 0.0 4 0 0 0 0 10 187 4 0.0 4 1 0 0 0 3 189 1 0.0 4 0 0 0 0 1 192 1 0.0 4 0 0 0 0 1 202 1 0.0 4 0 0 0 0 1 203 1 0.0 4 0 0 0 0 1 209 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 1 227 17 0.0 4 0 0 0 0 17 228 9 0.0 4 0 0 0 0 9 229 1 0.0 4 0 0 0 1 230 2 0.0 4 0 0 0 0 2 233 1 0.0 4 0 0 0 0 1 235 2 0.0 4 0 0 0 0 2 236 2 0.0 4 0 0 0 0 2 237 1 0.0 4 0 0 0 1 250 1 0.0 4 0 1 276 1 0.0 4 0 0 0 0 1 283 3 0.0 4 0 0 0 0 3 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 3.33 s (53 us/read; 1.13 M reads/minute). === Summary === Total reads processed: 62,874 Reads with adapters: 3,675 (5.8%) Reads written (passing filters): 62,874 (100.0%) Total basepairs processed: 13,799,738 bp Total written (filtered): 13,762,278 bp (99.7%) === Adapter 1 === Sequence: CTGSTGCVYCCCRTAGG; Type: regular 3'; Length: 17; Trimmed: 3675 times. No. of allowed errors: 0-9 bp: 0; 10-17 bp: 1 Bases preceding removed adapters: A: 11.9% C: 2.5% G: 83.6% T: 2.0% 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 3 116 982.4 0 116 4 180 245.6 0 180 5 5 61.4 0 5 6 4 15.4 0 4 9 1076 0.2 0 26 1050 10 1922 0.1 1 63 1859 11 242 0.0 1 5 237 12 1 0.0 1 0 1 13 2 0.0 1 0 2 17 2 0.0 1 2 18 95 0.0 1 74 21 19 5 0.0 1 4 1 20 1 0.0 1 1 22 1 0.0 1 1 56 1 0.0 1 0 1 70 1 0.0 1 0 1 80 1 0.0 1 1 122 1 0.0 1 1 128 1 0.0 1 0 1 129 16 0.0 1 14 2 130 1 0.0 1 1 208 1 0.0 1 0 1 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.