SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_BSr1_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.9 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 5205). Second best hit was smallRNA (count: 0) 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 Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.8 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC LCo_BSr1_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 459.179 s (4.592 µs/read; 13.07 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 46,925,421 (46.9%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 29,324,805 bp (0.2%) Total written (filtered): 14,996,587,532 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46925421 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.5% C: 16.9% G: 0.4% T: 33.1% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 45986328 25000000.0 0 45986328 2 92258 6250000.0 0 92258 3 64446 1562500.0 0 64446 4 45898 390625.0 0 45898 5 43252 97656.2 0 43252 6 36315 24414.1 0 36315 7 31813 6103.5 0 31813 8 37038 1525.9 0 37038 9 19592 381.5 0 19543 49 10 31360 95.4 1 26433 4927 11 24560 23.8 1 20472 4088 12 27045 6.0 1 22716 4329 13 24120 1.5 1 20518 3602 14 26841 1.5 1 22490 4351 15 17735 1.5 1 15096 2639 16 19334 1.5 1 16340 2994 17 23945 1.5 1 20580 3365 18 10759 1.5 1 9176 1583 19 20300 1.5 1 17548 2752 20 16795 1.5 1 14591 2204 21 8354 1.5 1 7219 1135 22 13328 1.5 1 11668 1660 23 12406 1.5 1 10762 1644 24 14678 1.5 1 12717 1961 25 13135 1.5 1 11587 1548 26 8023 1.5 1 6894 1129 27 5813 1.5 1 5007 806 28 9653 1.5 1 8603 1050 29 6778 1.5 1 6013 765 30 8131 1.5 1 7291 840 31 6381 1.5 1 5658 723 32 7072 1.5 1 6336 736 33 5896 1.5 1 5254 642 34 6731 1.5 1 6093 638 35 4753 1.5 1 4339 414 36 4994 1.5 1 4560 434 37 4706 1.5 1 4301 405 38 5271 1.5 1 4783 488 39 3811 1.5 1 3419 392 40 3928 1.5 1 3573 355 41 3687 1.5 1 3393 294 42 3901 1.5 1 3625 276 43 2886 1.5 1 2657 229 44 3257 1.5 1 3015 242 45 3261 1.5 1 2979 282 46 2852 1.5 1 2601 251 47 2563 1.5 1 2398 165 48 2515 1.5 1 2331 184 49 2466 1.5 1 2281 185 50 2200 1.5 1 2079 121 51 2003 1.5 1 1854 149 52 2076 1.5 1 1950 126 53 1969 1.5 1 1836 133 54 2167 1.5 1 2040 127 55 1368 1.5 1 1278 90 56 1745 1.5 1 1652 93 57 2095 1.5 1 1974 121 58 976 1.5 1 915 61 59 1311 1.5 1 1254 57 60 1430 1.5 1 1349 81 61 1390 1.5 1 1323 67 62 1123 1.5 1 1041 82 63 1955 1.5 1 1834 121 64 1033 1.5 1 979 54 65 863 1.5 1 820 43 66 664 1.5 1 628 36 67 1107 1.5 1 1057 50 68 995 1.5 1 952 43 69 868 1.5 1 819 49 70 955 1.5 1 912 43 71 846 1.5 1 794 52 72 907 1.5 1 865 42 73 1201 1.5 1 1149 52 74 857 1.5 1 821 36 75 489 1.5 1 463 26 76 315 1.5 1 282 33 77 488 1.5 1 456 32 78 727 1.5 1 592 135 79 600 1.5 1 531 69 80 568 1.5 1 524 44 81 531 1.5 1 504 27 82 530 1.5 1 505 25 83 496 1.5 1 472 24 84 495 1.5 1 466 29 85 477 1.5 1 453 24 86 457 1.5 1 430 27 87 418 1.5 1 390 28 88 422 1.5 1 398 24 89 403 1.5 1 387 16 90 354 1.5 1 337 17 91 356 1.5 1 334 22 92 345 1.5 1 327 18 93 349 1.5 1 335 14 94 311 1.5 1 293 18 95 324 1.5 1 306 18 96 306 1.5 1 298 8 97 308 1.5 1 292 16 98 329 1.5 1 314 15 99 271 1.5 1 259 12 100 264 1.5 1 249 15 101 292 1.5 1 278 14 102 262 1.5 1 246 16 103 265 1.5 1 252 13 104 302 1.5 1 284 18 105 239 1.5 1 226 13 106 244 1.5 1 226 18 107 217 1.5 1 195 22 108 198 1.5 1 185 13 109 203 1.5 1 190 13 110 200 1.5 1 182 18 111 189 1.5 1 171 18 112 178 1.5 1 155 23 113 195 1.5 1 168 27 114 206 1.5 1 176 30 115 219 1.5 1 186 33 116 217 1.5 1 190 27 117 237 1.5 1 192 45 118 242 1.5 1 180 62 119 283 1.5 1 204 79 120 327 1.5 1 175 152 121 467 1.5 1 250 217 122 540 1.5 1 267 273 123 700 1.5 1 293 407 124 1144 1.5 1 490 654 125 1055 1.5 1 276 779 126 1326 1.5 1 316 1010 127 1482 1.5 1 255 1227 128 1754 1.5 1 277 1477 129 1745 1.5 1 333 1412 130 1931 1.5 1 586 1345 131 1404 1.5 1 285 1119 132 1303 1.5 1 298 1005 133 1013 1.5 1 288 725 134 993 1.5 1 283 710 135 997 1.5 1 286 711 136 938 1.5 1 235 703 137 928 1.5 1 270 658 138 797 1.5 1 220 577 139 734 1.5 1 216 518 140 562 1.5 1 198 364 141 421 1.5 1 193 228 142 366 1.5 1 212 154 143 224 1.5 1 136 88 144 439 1.5 1 347 92 145 443 1.5 1 345 98 146 538 1.5 1 462 76 147 559 1.5 1 488 71 148 272 1.5 1 252 20 149 10176 1.5 1 10056 120 150 1733 1.5 1 1686 47 151 57721 1.5 1 57085 636 RUN STATISTICS FOR INPUT FILE: LCo_BSr1_2.fastq.gz ============================================= 100000000 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 100000000 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 133258 (0.13%)