SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_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: 5704). 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 LCo_BSr2_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 431.315 s (4.313 µs/read; 13.91 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,613,076 (43.6%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 13,148,311 bp (0.1%) Total written (filtered): 14,998,006,631 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43613076 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.0% C: 2.1% G: 11.3% T: 44.4% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 35052476 25000000.0 0 35052476 2 4870898 6250000.0 0 4870898 3 2010444 1562500.0 0 2010444 4 796108 390625.0 0 796108 5 48600 97656.2 0 48600 6 45031 24414.1 0 45031 7 37367 6103.5 0 37367 8 42779 1525.9 0 42779 9 31107 381.5 0 30436 671 10 33283 95.4 1 31091 2192 11 33750 23.8 1 31208 2542 12 30416 6.0 1 28919 1497 13 26637 1.5 1 25493 1144 14 25948 1.5 1 24237 1711 15 26169 1.5 1 24987 1182 16 20876 1.5 1 19604 1272 17 23175 1.5 1 21546 1629 18 25893 1.5 1 24758 1135 19 10160 1.5 1 9665 495 20 17583 1.5 1 16760 823 21 16391 1.5 1 15592 799 22 13874 1.5 1 13323 551 23 15512 1.5 1 14663 849 24 13008 1.5 1 12108 900 25 13009 1.5 1 12446 563 26 9900 1.5 1 9436 464 27 11337 1.5 1 10739 598 28 10430 1.5 1 9954 476 29 9379 1.5 1 8799 580 30 10681 1.5 1 10285 396 31 5639 1.5 1 5392 247 32 8372 1.5 1 8049 323 33 6696 1.5 1 6346 350 34 6969 1.5 1 6642 327 35 6456 1.5 1 6171 285 36 6838 1.5 1 6408 430 37 5939 1.5 1 5671 268 38 4880 1.5 1 4669 211 39 4596 1.5 1 4370 226 40 5585 1.5 1 5328 257 41 4312 1.5 1 4134 178 42 3993 1.5 1 3838 155 43 4266 1.5 1 4008 258 44 3372 1.5 1 3182 190 45 5638 1.5 1 5452 186 46 1075 1.5 1 1002 73 47 3025 1.5 1 2944 81 48 3633 1.5 1 3486 147 49 2367 1.5 1 2270 97 50 2647 1.5 1 2525 122 51 2676 1.5 1 2533 143 52 2509 1.5 1 2408 101 53 2301 1.5 1 2206 95 54 2255 1.5 1 2153 102 55 3158 1.5 1 3037 121 56 1207 1.5 1 1127 80 57 2385 1.5 1 2297 88 58 2378 1.5 1 2292 86 59 978 1.5 1 904 74 60 1957 1.5 1 1914 43 61 959 1.5 1 914 45 62 1685 1.5 1 1610 75 63 1950 1.5 1 1905 45 64 1367 1.5 1 1319 48 65 796 1.5 1 756 40 66 1462 1.5 1 1417 45 67 1578 1.5 1 1516 62 68 1800 1.5 1 1727 73 69 1441 1.5 1 1376 65 70 1667 1.5 1 1582 85 71 193 1.5 1 168 25 72 301 1.5 1 284 17 73 782 1.5 1 755 27 74 904 1.5 1 870 34 75 811 1.5 1 778 33 76 907 1.5 1 866 41 77 919 1.5 1 837 82 78 1174 1.5 1 929 245 79 979 1.5 1 846 133 80 814 1.5 1 740 74 81 780 1.5 1 743 37 82 712 1.5 1 679 33 83 696 1.5 1 667 29 84 730 1.5 1 704 26 85 674 1.5 1 639 35 86 643 1.5 1 615 28 87 646 1.5 1 623 23 88 575 1.5 1 550 25 89 560 1.5 1 532 28 90 572 1.5 1 551 21 91 489 1.5 1 474 15 92 531 1.5 1 513 18 93 501 1.5 1 485 16 94 489 1.5 1 469 20 95 527 1.5 1 505 22 96 448 1.5 1 430 18 97 435 1.5 1 414 21 98 430 1.5 1 409 21 99 388 1.5 1 370 18 100 438 1.5 1 424 14 101 411 1.5 1 400 11 102 416 1.5 1 409 7 103 383 1.5 1 361 22 104 514 1.5 1 493 21 105 358 1.5 1 346 12 106 367 1.5 1 349 18 107 347 1.5 1 330 17 108 320 1.5 1 309 11 109 298 1.5 1 287 11 110 303 1.5 1 294 9 111 314 1.5 1 303 11 112 337 1.5 1 325 12 113 314 1.5 1 296 18 114 313 1.5 1 301 12 115 299 1.5 1 287 12 116 359 1.5 1 350 9 117 353 1.5 1 346 7 118 378 1.5 1 370 8 119 388 1.5 1 377 11 120 446 1.5 1 437 9 121 573 1.5 1 556 17 122 687 1.5 1 665 22 123 659 1.5 1 646 13 124 709 1.5 1 695 14 125 699 1.5 1 690 9 126 653 1.5 1 648 5 127 526 1.5 1 516 10 128 400 1.5 1 391 9 129 393 1.5 1 388 5 130 302 1.5 1 296 6 131 256 1.5 1 253 3 132 332 1.5 1 325 7 133 291 1.5 1 280 11 134 319 1.5 1 312 7 135 247 1.5 1 240 7 136 233 1.5 1 223 10 137 247 1.5 1 235 12 138 239 1.5 1 227 12 139 269 1.5 1 264 5 140 243 1.5 1 233 10 141 287 1.5 1 279 8 142 343 1.5 1 325 18 143 240 1.5 1 226 14 144 619 1.5 1 593 26 145 566 1.5 1 543 23 146 788 1.5 1 735 53 147 823 1.5 1 778 45 148 406 1.5 1 375 31 149 13032 1.5 1 12551 481 150 3079 1.5 1 2878 201 151 93322 1.5 1 86675 6647 RUN STATISTICS FOR INPUT FILE: LCo_BSr2_1.fastq.gz ============================================= 100000000 sequences processed in total