SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_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: 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_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 408.773 s (4.088 µs/read; 14.68 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 47,461,624 (47.5%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 28,088,314 bp (0.2%) Total written (filtered): 14,989,763,664 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 47461624 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.9% C: 16.9% G: 0.3% T: 32.7% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 46380893 25000000.0 0 46380893 2 88902 6250000.0 0 88902 3 65252 1562500.0 0 65252 4 49479 390625.0 0 49479 5 47152 97656.2 0 47152 6 39128 24414.1 0 39128 7 34115 6103.5 0 34115 8 40291 1525.9 0 40291 9 20938 381.5 0 20881 57 10 34802 95.4 1 28911 5891 11 27432 23.8 1 22468 4964 12 30113 6.0 1 24794 5319 13 27024 1.5 1 22577 4447 14 29742 1.5 1 24500 5242 15 20022 1.5 1 16816 3206 16 22274 1.5 1 18551 3723 17 27965 1.5 1 23707 4258 18 12157 1.5 1 10125 2032 19 23894 1.5 1 20433 3461 20 18768 1.5 1 16051 2717 21 9611 1.5 1 8209 1402 22 15443 1.5 1 13245 2198 23 14483 1.5 1 12479 2004 24 17286 1.5 1 14749 2537 25 15485 1.5 1 13515 1970 26 9888 1.5 1 8416 1472 27 7207 1.5 1 6105 1102 28 12011 1.5 1 10471 1540 29 8000 1.5 1 6997 1003 30 11312 1.5 1 10050 1262 31 7002 1.5 1 6143 859 32 10414 1.5 1 9248 1166 33 5617 1.5 1 4842 775 34 9197 1.5 1 8334 863 35 4993 1.5 1 4481 512 36 7904 1.5 1 6966 938 37 7273 1.5 1 6684 589 38 5578 1.5 1 5036 542 39 5341 1.5 1 4777 564 40 3462 1.5 1 3104 358 41 5100 1.5 1 4579 521 42 5192 1.5 1 4768 424 43 3835 1.5 1 3464 371 44 4195 1.5 1 3832 363 45 4260 1.5 1 3859 401 46 3898 1.5 1 3537 361 47 3419 1.5 1 3158 261 48 3249 1.5 1 3004 245 49 3383 1.5 1 3075 308 50 3062 1.5 1 2894 168 51 2776 1.5 1 2559 217 52 2926 1.5 1 2693 233 53 2712 1.5 1 2526 186 54 3064 1.5 1 2869 195 55 1986 1.5 1 1830 156 56 2526 1.5 1 2357 169 57 3143 1.5 1 2963 180 58 1556 1.5 1 1424 132 59 1964 1.5 1 1859 105 60 2123 1.5 1 2010 113 61 2046 1.5 1 1908 138 62 1724 1.5 1 1631 93 63 2862 1.5 1 2692 170 64 1470 1.5 1 1389 81 65 1327 1.5 1 1237 90 66 1062 1.5 1 992 70 67 1687 1.5 1 1605 82 68 1563 1.5 1 1472 91 69 1246 1.5 1 1175 71 70 1447 1.5 1 1389 58 71 1443 1.5 1 1354 89 72 1470 1.5 1 1398 72 73 1963 1.5 1 1861 102 74 1402 1.5 1 1332 70 75 922 1.5 1 849 73 76 463 1.5 1 421 42 77 828 1.5 1 763 65 78 1128 1.5 1 932 196 79 1023 1.5 1 910 113 80 936 1.5 1 861 75 81 883 1.5 1 833 50 82 836 1.5 1 797 39 83 950 1.5 1 895 55 84 856 1.5 1 814 42 85 894 1.5 1 852 42 86 757 1.5 1 724 33 87 708 1.5 1 666 42 88 720 1.5 1 687 33 89 657 1.5 1 624 33 90 645 1.5 1 619 26 91 626 1.5 1 588 38 92 623 1.5 1 605 18 93 607 1.5 1 585 22 94 573 1.5 1 545 28 95 561 1.5 1 541 20 96 589 1.5 1 561 28 97 505 1.5 1 483 22 98 513 1.5 1 499 14 99 509 1.5 1 488 21 100 532 1.5 1 506 26 101 462 1.5 1 435 27 102 502 1.5 1 484 18 103 473 1.5 1 447 26 104 581 1.5 1 562 19 105 432 1.5 1 405 27 106 397 1.5 1 379 18 107 372 1.5 1 351 21 108 367 1.5 1 343 24 109 360 1.5 1 338 22 110 339 1.5 1 309 30 111 358 1.5 1 332 26 112 363 1.5 1 329 34 113 374 1.5 1 340 34 114 389 1.5 1 349 40 115 390 1.5 1 344 46 116 380 1.5 1 333 47 117 354 1.5 1 299 55 118 436 1.5 1 364 72 119 460 1.5 1 346 114 120 512 1.5 1 339 173 121 640 1.5 1 406 234 122 779 1.5 1 437 342 123 1017 1.5 1 487 530 124 1444 1.5 1 737 707 125 1364 1.5 1 494 870 126 1603 1.5 1 440 1163 127 1810 1.5 1 448 1362 128 2063 1.5 1 496 1567 129 2123 1.5 1 493 1630 130 2264 1.5 1 762 1502 131 1763 1.5 1 468 1295 132 1529 1.5 1 435 1094 133 1396 1.5 1 473 923 134 1202 1.5 1 357 845 135 1225 1.5 1 378 847 136 1202 1.5 1 380 822 137 1065 1.5 1 309 756 138 991 1.5 1 276 715 139 837 1.5 1 301 536 140 704 1.5 1 300 404 141 524 1.5 1 293 231 142 487 1.5 1 321 166 143 318 1.5 1 210 108 144 654 1.5 1 573 81 145 662 1.5 1 591 71 146 852 1.5 1 756 96 147 949 1.5 1 879 70 148 378 1.5 1 353 25 149 11558 1.5 1 11449 109 150 2441 1.5 1 2377 64 151 73704 1.5 1 72808 896 RUN STATISTICS FOR INPUT FILE: LCo_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): 160489 (0.16%)