SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_BSr3_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: 5703). 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 LYa_BSr3_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 421.598 s (4.216 µs/read; 14.23 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,035,985 (43.0%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 11,691,411 bp (0.1%) Total written (filtered): 15,000,140,635 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43035985 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.2% C: 1.9% G: 11.5% T: 45.2% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 34590248 25000000.0 0 34590248 2 4862216 6250000.0 0 4862216 3 1970926 1562500.0 0 1970926 4 800952 390625.0 0 800952 5 40863 97656.2 0 40863 6 37794 24414.1 0 37794 7 30827 6103.5 0 30827 8 35543 1525.9 0 35543 9 25783 381.5 0 25094 689 10 27465 95.4 1 25391 2074 11 28271 23.8 1 26026 2245 12 25361 6.0 1 23983 1378 13 23574 1.5 1 22503 1071 14 20656 1.5 1 19250 1406 15 22316 1.5 1 21227 1089 16 17225 1.5 1 16049 1176 17 19751 1.5 1 18289 1462 18 22320 1.5 1 21339 981 19 8606 1.5 1 8141 465 20 15343 1.5 1 14577 766 21 14141 1.5 1 13407 734 22 12129 1.5 1 11614 515 23 14042 1.5 1 13263 779 24 10992 1.5 1 10151 841 25 11774 1.5 1 11208 566 26 8793 1.5 1 8407 386 27 10099 1.5 1 9557 542 28 9548 1.5 1 9124 424 29 8564 1.5 1 7973 591 30 10430 1.5 1 9986 444 31 4981 1.5 1 4753 228 32 7506 1.5 1 7156 350 33 6702 1.5 1 6336 366 34 6829 1.5 1 6423 406 35 6619 1.5 1 6349 270 36 5233 1.5 1 4960 273 37 6476 1.5 1 6080 396 38 6073 1.5 1 5851 222 39 3738 1.5 1 3580 158 40 5412 1.5 1 5155 257 41 5582 1.5 1 5279 303 42 3610 1.5 1 3479 131 43 4980 1.5 1 4654 326 44 2963 1.5 1 2792 171 45 6087 1.5 1 5883 204 46 1029 1.5 1 946 83 47 3328 1.5 1 3220 108 48 4003 1.5 1 3807 196 49 2584 1.5 1 2482 102 50 3108 1.5 1 2956 152 51 2924 1.5 1 2759 165 52 2871 1.5 1 2759 112 53 2787 1.5 1 2677 110 54 2728 1.5 1 2579 149 55 3573 1.5 1 3420 153 56 1524 1.5 1 1461 63 57 2730 1.5 1 2615 115 58 3222 1.5 1 3128 94 59 1181 1.5 1 1106 75 60 2523 1.5 1 2446 77 61 1349 1.5 1 1300 49 62 2117 1.5 1 2005 112 63 2369 1.5 1 2290 79 64 1989 1.5 1 1920 69 65 1014 1.5 1 968 46 66 1769 1.5 1 1690 79 67 2217 1.5 1 2124 93 68 2473 1.5 1 2374 99 69 1857 1.5 1 1772 85 70 2403 1.5 1 2281 122 71 241 1.5 1 221 20 72 401 1.5 1 383 18 73 999 1.5 1 955 44 74 1229 1.5 1 1195 34 75 1278 1.5 1 1225 53 76 1235 1.5 1 1191 44 77 1350 1.5 1 1260 90 78 1562 1.5 1 1300 262 79 1398 1.5 1 1250 148 80 1253 1.5 1 1168 85 81 1157 1.5 1 1099 58 82 1122 1.5 1 1076 46 83 1119 1.5 1 1075 44 84 1028 1.5 1 984 44 85 1052 1.5 1 1019 33 86 973 1.5 1 929 44 87 959 1.5 1 915 44 88 989 1.5 1 953 36 89 935 1.5 1 892 43 90 821 1.5 1 788 33 91 851 1.5 1 815 36 92 810 1.5 1 776 34 93 803 1.5 1 780 23 94 818 1.5 1 777 41 95 804 1.5 1 780 24 96 826 1.5 1 801 25 97 707 1.5 1 680 27 98 725 1.5 1 708 17 99 722 1.5 1 693 29 100 700 1.5 1 673 27 101 683 1.5 1 663 20 102 659 1.5 1 638 21 103 647 1.5 1 628 19 104 792 1.5 1 765 27 105 589 1.5 1 570 19 106 599 1.5 1 583 16 107 610 1.5 1 594 16 108 599 1.5 1 584 15 109 591 1.5 1 567 24 110 542 1.5 1 525 17 111 518 1.5 1 500 18 112 511 1.5 1 494 17 113 505 1.5 1 485 20 114 513 1.5 1 493 20 115 530 1.5 1 511 19 116 514 1.5 1 497 17 117 517 1.5 1 501 16 118 542 1.5 1 519 23 119 563 1.5 1 548 15 120 627 1.5 1 605 22 121 713 1.5 1 695 18 122 817 1.5 1 803 14 123 874 1.5 1 854 20 124 938 1.5 1 916 22 125 877 1.5 1 853 24 126 770 1.5 1 754 16 127 630 1.5 1 620 10 128 548 1.5 1 542 6 129 555 1.5 1 540 15 130 441 1.5 1 432 9 131 397 1.5 1 387 10 132 442 1.5 1 432 10 133 496 1.5 1 484 12 134 472 1.5 1 455 17 135 430 1.5 1 408 22 136 422 1.5 1 407 15 137 360 1.5 1 343 17 138 349 1.5 1 341 8 139 420 1.5 1 405 15 140 367 1.5 1 346 21 141 381 1.5 1 367 14 142 423 1.5 1 398 25 143 347 1.5 1 325 22 144 631 1.5 1 599 32 145 963 1.5 1 881 82 146 1333 1.5 1 1236 97 147 1370 1.5 1 1288 82 148 468 1.5 1 436 32 149 13818 1.5 1 13270 548 150 2596 1.5 1 2428 168 151 82804 1.5 1 76641 6163 RUN STATISTICS FOR INPUT FILE: LYa_BSr3_1.fastq.gz ============================================= 100000000 sequences processed in total