SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_BSr3_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: 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_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 417.530 s (4.175 µs/read; 14.37 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 46,305,770 (46.3%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 37,188,303 bp (0.2%) Total written (filtered): 14,982,387,475 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46305770 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.1% C: 17.6% G: 0.4% T: 32.8% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 45338270 25000000.0 0 45338270 2 100901 6250000.0 0 100901 3 60832 1562500.0 0 60832 4 40696 390625.0 0 40696 5 38302 97656.2 0 38302 6 31849 24414.1 0 31849 7 28294 6103.5 0 28294 8 32608 1525.9 0 32608 9 15994 381.5 0 15940 54 10 28364 95.4 1 23593 4771 11 21251 23.8 1 17491 3760 12 23921 6.0 1 19805 4116 13 21515 1.5 1 18087 3428 14 24745 1.5 1 20477 4268 15 14559 1.5 1 12350 2209 16 17919 1.5 1 14962 2957 17 20646 1.5 1 17604 3042 18 10929 1.5 1 9259 1670 19 16339 1.5 1 13857 2482 20 16706 1.5 1 14320 2386 21 9314 1.5 1 8015 1299 22 12307 1.5 1 10574 1733 23 11801 1.5 1 10222 1579 24 13826 1.5 1 11891 1935 25 12348 1.5 1 10758 1590 26 7912 1.5 1 6719 1193 27 6432 1.5 1 5499 933 28 9275 1.5 1 8174 1101 29 7287 1.5 1 6434 853 30 8879 1.5 1 7877 1002 31 6377 1.5 1 5613 764 32 6932 1.5 1 6134 798 33 6893 1.5 1 6045 848 34 6267 1.5 1 5533 734 35 6231 1.5 1 5682 549 36 4988 1.5 1 4458 530 37 5552 1.5 1 4972 580 38 6453 1.5 1 5848 605 39 4596 1.5 1 4098 498 40 4893 1.5 1 4466 427 41 3327 1.5 1 2953 374 42 4506 1.5 1 4175 331 43 3720 1.5 1 3372 348 44 3826 1.5 1 3519 307 45 3958 1.5 1 3584 374 46 3445 1.5 1 3119 326 47 3172 1.5 1 2973 199 48 3216 1.5 1 2957 259 49 3091 1.5 1 2832 259 50 2997 1.5 1 2771 226 51 2651 1.5 1 2455 196 52 2788 1.5 1 2576 212 53 2733 1.5 1 2532 201 54 3125 1.5 1 2921 204 55 1876 1.5 1 1740 136 56 2548 1.5 1 2353 195 57 3237 1.5 1 3034 203 58 1508 1.5 1 1367 141 59 1913 1.5 1 1823 90 60 2236 1.5 1 2101 135 61 2175 1.5 1 2051 124 62 1742 1.5 1 1617 125 63 3312 1.5 1 3103 209 64 1565 1.5 1 1496 69 65 1320 1.5 1 1245 75 66 1033 1.5 1 963 70 67 1931 1.5 1 1829 102 68 1620 1.5 1 1533 87 69 1509 1.5 1 1432 77 70 1712 1.5 1 1631 81 71 1538 1.5 1 1453 85 72 1595 1.5 1 1500 95 73 2283 1.5 1 2152 131 74 1473 1.5 1 1374 99 75 1040 1.5 1 941 99 76 538 1.5 1 497 41 77 1059 1.5 1 993 66 78 1251 1.5 1 1085 166 79 1213 1.5 1 1108 105 80 1140 1.5 1 1064 76 81 1101 1.5 1 1048 53 82 1103 1.5 1 1047 56 83 1089 1.5 1 1033 56 84 1000 1.5 1 951 49 85 1056 1.5 1 1010 46 86 966 1.5 1 920 46 87 926 1.5 1 891 35 88 947 1.5 1 900 47 89 893 1.5 1 857 36 90 805 1.5 1 766 39 91 828 1.5 1 790 38 92 793 1.5 1 751 42 93 792 1.5 1 762 30 94 786 1.5 1 756 30 95 782 1.5 1 757 25 96 803 1.5 1 772 31 97 681 1.5 1 654 27 98 719 1.5 1 694 25 99 727 1.5 1 699 28 100 691 1.5 1 657 34 101 682 1.5 1 652 30 102 635 1.5 1 607 28 103 626 1.5 1 597 29 104 762 1.5 1 723 39 105 577 1.5 1 540 37 106 587 1.5 1 556 31 107 592 1.5 1 571 21 108 610 1.5 1 577 33 109 567 1.5 1 531 36 110 521 1.5 1 504 17 111 521 1.5 1 482 39 112 509 1.5 1 480 29 113 501 1.5 1 462 39 114 508 1.5 1 475 33 115 511 1.5 1 480 31 116 507 1.5 1 462 45 117 498 1.5 1 452 46 118 542 1.5 1 479 63 119 549 1.5 1 456 93 120 582 1.5 1 457 125 121 663 1.5 1 468 195 122 800 1.5 1 524 276 123 962 1.5 1 577 385 124 1322 1.5 1 766 556 125 1319 1.5 1 585 734 126 1471 1.5 1 561 910 127 1605 1.5 1 502 1103 128 1885 1.5 1 590 1295 129 1958 1.5 1 567 1391 130 2067 1.5 1 799 1268 131 1710 1.5 1 542 1168 132 1503 1.5 1 561 942 133 1447 1.5 1 641 806 134 1294 1.5 1 553 741 135 1314 1.5 1 537 777 136 1321 1.5 1 491 830 137 1179 1.5 1 442 737 138 1061 1.5 1 398 663 139 977 1.5 1 432 545 140 783 1.5 1 402 381 141 683 1.5 1 397 286 142 563 1.5 1 424 139 143 433 1.5 1 338 95 144 714 1.5 1 607 107 145 1043 1.5 1 931 112 146 1382 1.5 1 1287 95 147 1387 1.5 1 1314 73 148 430 1.5 1 394 36 149 13643 1.5 1 13475 168 150 2106 1.5 1 2025 81 151 73745 1.5 1 72740 1005 RUN STATISTICS FOR INPUT FILE: LYa_BSr3_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): 166850 (0.17%)