SUMMARISING RUN PARAMETERS ========================== Input filename: WGBS-Col-0-GSM2136441-SRR3465232_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.15 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.15 with Python 2.7.14+ Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC WGBS-Col-0-GSM2136441-SRR3465232_2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2976.45 s (40 us/read; 1.51 M reads/minute). === Summary === Total reads processed: 74,711,902 Reads with adapters: 15,221,614 (20.4%) Reads written (passing filters): 74,711,902 (100.0%) Total basepairs processed: 10,890,898,269 bp Quality-trimmed: 238,569,156 bp (2.2%) Total written (filtered): 10,625,441,315 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15221614 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.4% C: 26.6% G: 24.4% T: 13.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 10431089 18677975.5 0 10431089 2 3190309 4669493.9 0 3190309 3 1190485 1167373.5 0 1190485 4 149057 291843.4 0 149057 5 73984 72960.8 0 73984 6 23046 18240.2 0 23046 7 16759 4560.1 0 16759 8 2610 1140.0 0 2610 9 3859 285.0 0 2010 1849 10 7140 71.3 1 2119 5021 11 6005 17.8 1 1348 4657 12 6330 4.5 1 1924 4406 13 5318 1.1 1 1753 3565 14 19151 1.1 1 5331 13820 15 3554 1.1 1 649 2905 16 5725 1.1 1 546 5179 17 9791 1.1 1 2463 7328 18 2720 1.1 1 789 1931 19 5544 1.1 1 1211 4333 20 1454 1.1 1 232 1222 21 775 1.1 1 105 670 22 751 1.1 1 146 605 23 2910 1.1 1 585 2325 24 7004 1.1 1 1615 5389 25 2357 1.1 1 531 1826 26 3499 1.1 1 817 2682 27 1258 1.1 1 339 919 28 1800 1.1 1 480 1320 29 903 1.1 1 194 709 30 1654 1.1 1 506 1148 31 834 1.1 1 193 641 32 1394 1.1 1 341 1053 33 1302 1.1 1 315 987 34 448 1.1 1 69 379 35 492 1.1 1 63 429 36 599 1.1 1 138 461 37 360 1.1 1 86 274 38 859 1.1 1 166 693 39 679 1.1 1 144 535 40 989 1.1 1 227 762 41 641 1.1 1 165 476 42 1135 1.1 1 276 859 43 460 1.1 1 74 386 44 866 1.1 1 172 694 45 727 1.1 1 151 576 46 348 1.1 1 59 289 47 283 1.1 1 22 261 48 340 1.1 1 59 281 49 343 1.1 1 13 330 50 285 1.1 1 40 245 51 327 1.1 1 45 282 52 406 1.1 1 20 386 53 258 1.1 1 11 247 54 287 1.1 1 12 275 55 420 1.1 1 42 378 56 350 1.1 1 16 334 57 808 1.1 1 13 795 58 353 1.1 1 38 315 59 355 1.1 1 18 337 60 252 1.1 1 37 215 61 277 1.1 1 34 243 62 406 1.1 1 15 391 63 610 1.1 1 24 586 64 363 1.1 1 23 340 65 502 1.1 1 18 484 66 299 1.1 1 43 256 67 573 1.1 1 14 559 68 306 1.1 1 23 283 69 348 1.1 1 45 303 70 363 1.1 1 22 341 71 317 1.1 1 20 297 72 339 1.1 1 15 324 73 179 1.1 1 10 169 74 153 1.1 1 8 145 75 207 1.1 1 14 193 76 489 1.1 1 8 481 77 219 1.1 1 4 215 78 332 1.1 1 3 329 79 193 1.1 1 5 188 80 262 1.1 1 6 256 81 456 1.1 1 5 451 82 255 1.1 1 8 247 83 273 1.1 1 3 270 84 254 1.1 1 12 242 85 118 1.1 1 6 112 86 137 1.1 1 4 133 87 327 1.1 1 1 326 88 459 1.1 1 3 456 89 266 1.1 1 3 263 90 386 1.1 1 3 383 91 245 1.1 1 1 244 92 590 1.1 1 3 587 93 268 1.1 1 4 264 94 267 1.1 1 8 259 95 192 1.1 1 3 189 96 170 1.1 1 2 168 97 311 1.1 1 9 302 98 219 1.1 1 3 216 99 278 1.1 1 5 273 100 304 1.1 1 4 300 101 712 1.1 1 8 704 102 263 1.1 1 6 257 103 448 1.1 1 4 444 104 147 1.1 1 4 143 105 135 1.1 1 4 131 106 157 1.1 1 7 150 107 212 1.1 1 1 211 108 206 1.1 1 4 202 109 175 1.1 1 1 174 110 530 1.1 1 1 529 111 303 1.1 1 5 298 112 398 1.1 1 2 396 113 140 1.1 1 4 136 114 164 1.1 1 2 162 115 322 1.1 1 5 317 116 236 1.1 1 1 235 117 208 1.1 1 2 206 118 189 1.1 1 2 187 119 774 1.1 1 6 768 120 159 1.1 1 2 157 121 269 1.1 1 3 266 122 442 1.1 1 2 440 123 174 1.1 1 1 173 124 275 1.1 1 2 273 125 203 1.1 1 0 203 126 730 1.1 1 1 729 127 278 1.1 1 1 277 128 380 1.1 1 1 379 129 229 1.1 1 0 229 130 135 1.1 1 1 134 131 565 1.1 1 1 564 132 195 1.1 1 0 195 133 1264 1.1 1 9 1255 134 210 1.1 1 1 209 135 604 1.1 1 4 600 136 141 1.1 1 0 141 137 116 1.1 1 0 116 138 148 1.1 1 1 147 139 267 1.1 1 2 265 140 170 1.1 1 0 170 141 228 1.1 1 0 228 142 243 1.1 1 1 242 143 247 1.1 1 0 247 144 143 1.1 1 0 143 145 93 1.1 1 1 92 146 275 1.1 1 0 275 147 230 1.1 1 0 230 148 196 1.1 1 0 196 149 132 1.1 1 0 132 150 240 1.1 1 0 240 151 361 1.1 1 1 360 RUN STATISTICS FOR INPUT FILE: WGBS-Col-0-GSM2136441-SRR3465232_2.fastq.gz ============================================= 74711902 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 74711902 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 993171 (1.33%)