SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_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: 6353). 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_BSr3_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 417.070 s (4.171 µs/read; 14.39 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,101,993 (43.1%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 11,588,041 bp (0.1%) Total written (filtered): 14,999,007,491 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43101993 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.3% C: 2.2% G: 11.3% T: 45.0% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 34615945 25000000.0 0 34615945 2 4777475 6250000.0 0 4777475 3 1957820 1562500.0 0 1957820 4 802358 390625.0 0 802358 5 51147 97656.2 0 51147 6 46692 24414.1 0 46692 7 38963 6103.5 0 38963 8 44059 1525.9 0 44059 9 33846 381.5 0 33133 713 10 34962 95.4 1 32644 2318 11 35734 23.8 1 32921 2813 12 32341 6.0 1 30653 1688 13 28506 1.5 1 27169 1337 14 27357 1.5 1 25490 1867 15 27805 1.5 1 26285 1520 16 22757 1.5 1 21282 1475 17 25367 1.5 1 23441 1926 18 27599 1.5 1 26406 1193 19 11522 1.5 1 10933 589 20 18923 1.5 1 17917 1006 21 18020 1.5 1 17071 949 22 15401 1.5 1 14725 676 23 17499 1.5 1 16468 1031 24 13750 1.5 1 12691 1059 25 14633 1.5 1 13896 737 26 10795 1.5 1 10261 534 27 12519 1.5 1 11845 674 28 12010 1.5 1 11456 554 29 10043 1.5 1 9366 677 30 12173 1.5 1 11623 550 31 6568 1.5 1 6282 286 32 9868 1.5 1 9425 443 33 6997 1.5 1 6559 438 34 8162 1.5 1 7686 476 35 9663 1.5 1 9198 465 36 4352 1.5 1 4171 181 37 7060 1.5 1 6724 336 38 5679 1.5 1 5343 336 39 7732 1.5 1 7326 406 40 3878 1.5 1 3691 187 41 5426 1.5 1 5151 275 42 4981 1.5 1 4778 203 43 6348 1.5 1 5993 355 44 2986 1.5 1 2775 211 45 6779 1.5 1 6537 242 46 1344 1.5 1 1225 119 47 3605 1.5 1 3435 170 48 5395 1.5 1 5148 247 49 2388 1.5 1 2278 110 50 3632 1.5 1 3441 191 51 3072 1.5 1 2905 167 52 2910 1.5 1 2782 128 53 2646 1.5 1 2543 103 54 3879 1.5 1 3715 164 55 4120 1.5 1 3977 143 56 1072 1.5 1 992 80 57 3922 1.5 1 3821 101 58 1618 1.5 1 1545 73 59 1538 1.5 1 1469 69 60 1913 1.5 1 1867 46 61 589 1.5 1 551 38 62 2148 1.5 1 2058 90 63 3009 1.5 1 2948 61 64 751 1.5 1 722 29 65 812 1.5 1 775 37 66 1952 1.5 1 1884 68 67 1475 1.5 1 1419 56 68 1943 1.5 1 1867 76 69 1716 1.5 1 1630 86 70 2306 1.5 1 2221 85 71 233 1.5 1 209 24 72 299 1.5 1 287 12 73 726 1.5 1 701 25 74 962 1.5 1 942 20 75 1090 1.5 1 1043 47 76 1119 1.5 1 1075 44 77 1093 1.5 1 990 103 78 1449 1.5 1 1163 286 79 1213 1.5 1 1021 192 80 1014 1.5 1 936 78 81 945 1.5 1 900 45 82 873 1.5 1 823 50 83 937 1.5 1 905 32 84 847 1.5 1 816 31 85 853 1.5 1 818 35 86 758 1.5 1 731 27 87 721 1.5 1 682 39 88 754 1.5 1 727 27 89 693 1.5 1 671 22 90 683 1.5 1 651 32 91 663 1.5 1 627 36 92 642 1.5 1 629 13 93 637 1.5 1 619 18 94 613 1.5 1 578 35 95 587 1.5 1 561 26 96 607 1.5 1 595 12 97 532 1.5 1 515 17 98 536 1.5 1 515 21 99 513 1.5 1 492 21 100 527 1.5 1 508 19 101 471 1.5 1 454 17 102 533 1.5 1 520 13 103 502 1.5 1 481 21 104 626 1.5 1 594 32 105 448 1.5 1 426 22 106 424 1.5 1 410 14 107 402 1.5 1 380 22 108 389 1.5 1 374 15 109 379 1.5 1 367 12 110 355 1.5 1 336 19 111 383 1.5 1 374 9 112 362 1.5 1 354 8 113 412 1.5 1 393 19 114 439 1.5 1 427 12 115 437 1.5 1 416 21 116 440 1.5 1 424 16 117 459 1.5 1 441 18 118 496 1.5 1 475 21 119 566 1.5 1 551 15 120 602 1.5 1 593 9 121 724 1.5 1 713 11 122 795 1.5 1 769 26 123 822 1.5 1 806 16 124 865 1.5 1 854 11 125 804 1.5 1 793 11 126 802 1.5 1 788 14 127 676 1.5 1 665 11 128 512 1.5 1 503 9 129 467 1.5 1 459 8 130 419 1.5 1 414 5 131 343 1.5 1 331 12 132 392 1.5 1 383 9 133 385 1.5 1 380 5 134 316 1.5 1 297 19 135 312 1.5 1 297 15 136 303 1.5 1 295 8 137 266 1.5 1 257 9 138 267 1.5 1 253 14 139 321 1.5 1 308 13 140 288 1.5 1 277 11 141 277 1.5 1 269 8 142 353 1.5 1 332 21 143 240 1.5 1 229 11 144 630 1.5 1 607 23 145 655 1.5 1 620 35 146 830 1.5 1 798 32 147 969 1.5 1 928 41 148 457 1.5 1 422 35 149 11875 1.5 1 11474 401 150 3224 1.5 1 3013 211 151 85905 1.5 1 79719 6186 RUN STATISTICS FOR INPUT FILE: LCo_BSr3_1.fastq.gz ============================================= 100000000 sequences processed in total