SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_BSr2_1.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: 4945). Second best hit was Nextera (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 LYa_BSr2_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 448.300 s (4.483 µs/read; 13.38 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,278,899 (43.3%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 11,617,018 bp (0.1%) Total written (filtered): 15,003,286,991 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43278899 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.5% C: 1.6% G: 11.4% T: 45.3% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 34901851 25000000.0 0 34901851 2 4892863 6250000.0 0 4892863 3 1982350 1562500.0 0 1982350 4 802901 390625.0 0 802901 5 36051 97656.2 0 36051 6 33092 24414.1 0 33092 7 27396 6103.5 0 27396 8 30829 1525.9 0 30829 9 23161 381.5 0 22484 677 10 23969 95.4 1 22090 1879 11 24686 23.8 1 22661 2025 12 22142 6.0 1 20923 1219 13 19920 1.5 1 19083 837 14 18042 1.5 1 16803 1239 15 19151 1.5 1 18219 932 16 15352 1.5 1 14361 991 17 17061 1.5 1 15783 1278 18 19568 1.5 1 18707 861 19 7134 1.5 1 6762 372 20 12870 1.5 1 12235 635 21 12113 1.5 1 11466 647 22 10271 1.5 1 9846 425 23 12087 1.5 1 11427 660 24 9331 1.5 1 8656 675 25 10153 1.5 1 9672 481 26 7189 1.5 1 6857 332 27 8572 1.5 1 8062 510 28 8043 1.5 1 7721 322 29 7349 1.5 1 6891 458 30 8527 1.5 1 8209 318 31 4021 1.5 1 3848 173 32 6413 1.5 1 6125 288 33 5499 1.5 1 5161 338 34 6123 1.5 1 5833 290 35 4945 1.5 1 4766 179 36 4565 1.5 1 4212 353 37 5294 1.5 1 5093 201 38 2905 1.5 1 2772 133 39 4124 1.5 1 3946 178 40 3878 1.5 1 3707 171 41 4096 1.5 1 3910 186 42 3790 1.5 1 3621 169 43 3163 1.5 1 2974 189 44 2782 1.5 1 2613 169 45 4875 1.5 1 4725 150 46 885 1.5 1 826 59 47 2489 1.5 1 2403 86 48 3191 1.5 1 3057 134 49 1912 1.5 1 1828 84 50 2399 1.5 1 2283 116 51 2353 1.5 1 2186 167 52 2167 1.5 1 2061 106 53 1992 1.5 1 1922 70 54 2099 1.5 1 2003 96 55 2760 1.5 1 2661 99 56 1052 1.5 1 988 64 57 2351 1.5 1 2267 84 58 1976 1.5 1 1895 81 59 1056 1.5 1 998 58 60 1571 1.5 1 1538 33 61 688 1.5 1 649 39 62 1652 1.5 1 1585 67 63 1914 1.5 1 1873 41 64 993 1.5 1 954 39 65 706 1.5 1 664 42 66 1424 1.5 1 1371 53 67 1371 1.5 1 1325 46 68 1594 1.5 1 1534 60 69 1332 1.5 1 1262 70 70 1721 1.5 1 1657 64 71 131 1.5 1 108 23 72 269 1.5 1 259 10 73 618 1.5 1 593 25 74 819 1.5 1 787 32 75 845 1.5 1 811 34 76 870 1.5 1 823 47 77 888 1.5 1 814 74 78 1117 1.5 1 902 215 79 1010 1.5 1 854 156 80 862 1.5 1 790 72 81 800 1.5 1 753 47 82 728 1.5 1 695 33 83 645 1.5 1 608 37 84 725 1.5 1 701 24 85 727 1.5 1 704 23 86 648 1.5 1 621 27 87 601 1.5 1 583 18 88 549 1.5 1 525 24 89 588 1.5 1 560 28 90 570 1.5 1 547 23 91 530 1.5 1 509 21 92 553 1.5 1 525 28 93 481 1.5 1 461 20 94 508 1.5 1 487 21 95 474 1.5 1 453 21 96 452 1.5 1 440 12 97 476 1.5 1 448 28 98 477 1.5 1 464 13 99 407 1.5 1 387 20 100 413 1.5 1 390 23 101 384 1.5 1 366 18 102 391 1.5 1 373 18 103 385 1.5 1 367 18 104 495 1.5 1 473 22 105 403 1.5 1 384 19 106 398 1.5 1 383 15 107 345 1.5 1 328 17 108 368 1.5 1 353 15 109 309 1.5 1 298 11 110 309 1.5 1 297 12 111 300 1.5 1 289 11 112 327 1.5 1 314 13 113 309 1.5 1 297 12 114 334 1.5 1 321 13 115 363 1.5 1 347 16 116 317 1.5 1 300 17 117 344 1.5 1 334 10 118 368 1.5 1 357 11 119 431 1.5 1 420 11 120 520 1.5 1 506 14 121 501 1.5 1 492 9 122 611 1.5 1 595 16 123 635 1.5 1 622 13 124 739 1.5 1 726 13 125 686 1.5 1 680 6 126 649 1.5 1 643 6 127 569 1.5 1 558 11 128 429 1.5 1 419 10 129 348 1.5 1 340 8 130 312 1.5 1 304 8 131 270 1.5 1 266 4 132 341 1.5 1 328 13 133 353 1.5 1 349 4 134 309 1.5 1 293 16 135 259 1.5 1 251 8 136 238 1.5 1 229 9 137 248 1.5 1 237 11 138 245 1.5 1 237 8 139 285 1.5 1 275 10 140 259 1.5 1 251 8 141 288 1.5 1 278 10 142 353 1.5 1 330 23 143 242 1.5 1 231 11 144 552 1.5 1 540 12 145 617 1.5 1 593 24 146 954 1.5 1 902 52 147 898 1.5 1 846 52 148 429 1.5 1 397 32 149 14487 1.5 1 13923 564 150 2894 1.5 1 2708 186 151 88573 1.5 1 82374 6199 RUN STATISTICS FOR INPUT FILE: LYa_BSr2_1.fastq.gz ============================================= 100000000 sequences processed in total