SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_BSr2_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: 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_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 437.522 s (4.375 µs/read; 13.71 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 46,731,941 (46.7%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 30,504,002 bp (0.2%) Total written (filtered): 14,989,383,352 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46731941 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.5% C: 17.0% G: 0.4% T: 33.0% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 45702359 25000000.0 0 45702359 2 98459 6250000.0 0 98459 3 65128 1562500.0 0 65128 4 48379 390625.0 0 48379 5 44707 97656.2 0 44707 6 37336 24414.1 0 37336 7 33672 6103.5 0 33672 8 39612 1525.9 0 39612 9 18359 381.5 0 18320 39 10 33686 95.4 1 27913 5773 11 25375 23.8 1 20880 4495 12 28414 6.0 1 23465 4949 13 25482 1.5 1 21234 4248 14 28149 1.5 1 23198 4951 15 18835 1.5 1 15901 2934 16 20674 1.5 1 17398 3276 17 26165 1.5 1 22237 3928 18 10926 1.5 1 9138 1788 19 22451 1.5 1 19145 3306 20 16989 1.5 1 14631 2358 21 8759 1.5 1 7492 1267 22 14070 1.5 1 12102 1968 23 13335 1.5 1 11510 1825 24 16616 1.5 1 14185 2431 25 13967 1.5 1 12132 1835 26 8605 1.5 1 7323 1282 27 6068 1.5 1 5105 963 28 10743 1.5 1 9454 1289 29 7217 1.5 1 6394 823 30 10441 1.5 1 9321 1120 31 5655 1.5 1 4928 727 32 9401 1.5 1 8369 1032 33 4845 1.5 1 4215 630 34 6717 1.5 1 5988 729 35 7622 1.5 1 6888 734 36 6572 1.5 1 5984 588 37 3091 1.5 1 2709 382 38 5824 1.5 1 5278 546 39 3944 1.5 1 3527 417 40 5165 1.5 1 4696 469 41 3568 1.5 1 3237 331 42 4173 1.5 1 3809 364 43 3613 1.5 1 3275 338 44 3588 1.5 1 3293 295 45 3655 1.5 1 3319 336 46 3335 1.5 1 3032 303 47 2797 1.5 1 2621 176 48 2832 1.5 1 2631 201 49 2832 1.5 1 2619 213 50 2510 1.5 1 2342 168 51 2472 1.5 1 2269 203 52 2455 1.5 1 2277 178 53 2237 1.5 1 2082 155 54 2523 1.5 1 2351 172 55 1638 1.5 1 1520 118 56 2104 1.5 1 1949 155 57 2454 1.5 1 2293 161 58 1272 1.5 1 1176 96 59 1548 1.5 1 1463 85 60 1765 1.5 1 1676 89 61 1678 1.5 1 1585 93 62 1334 1.5 1 1242 92 63 2356 1.5 1 2193 163 64 1237 1.5 1 1157 80 65 1090 1.5 1 1031 59 66 907 1.5 1 861 46 67 1332 1.5 1 1268 64 68 1222 1.5 1 1148 74 69 1126 1.5 1 1067 59 70 1178 1.5 1 1105 73 71 1051 1.5 1 985 66 72 1202 1.5 1 1136 66 73 1650 1.5 1 1565 85 74 1173 1.5 1 1123 50 75 768 1.5 1 714 54 76 366 1.5 1 322 44 77 725 1.5 1 663 62 78 898 1.5 1 725 173 79 818 1.5 1 722 96 80 729 1.5 1 656 73 81 740 1.5 1 700 40 82 680 1.5 1 648 32 83 709 1.5 1 675 34 84 701 1.5 1 670 31 85 685 1.5 1 645 40 86 658 1.5 1 621 37 87 617 1.5 1 581 36 88 557 1.5 1 524 33 89 525 1.5 1 499 26 90 550 1.5 1 524 26 91 463 1.5 1 439 24 92 524 1.5 1 499 25 93 488 1.5 1 471 17 94 456 1.5 1 443 13 95 508 1.5 1 492 16 96 427 1.5 1 407 20 97 415 1.5 1 395 20 98 416 1.5 1 396 20 99 382 1.5 1 367 15 100 443 1.5 1 420 23 101 409 1.5 1 393 16 102 388 1.5 1 371 17 103 359 1.5 1 341 18 104 477 1.5 1 462 15 105 339 1.5 1 317 22 106 357 1.5 1 340 17 107 327 1.5 1 306 21 108 322 1.5 1 292 30 109 282 1.5 1 263 19 110 288 1.5 1 270 18 111 287 1.5 1 270 17 112 318 1.5 1 294 24 113 302 1.5 1 269 33 114 278 1.5 1 262 16 115 278 1.5 1 247 31 116 307 1.5 1 275 32 117 308 1.5 1 265 43 118 344 1.5 1 290 54 119 327 1.5 1 272 55 120 339 1.5 1 242 97 121 467 1.5 1 291 176 122 638 1.5 1 398 240 123 841 1.5 1 467 374 124 1307 1.5 1 735 572 125 1110 1.5 1 469 641 126 1329 1.5 1 466 863 127 1406 1.5 1 408 998 128 1687 1.5 1 478 1209 129 1793 1.5 1 509 1284 130 2035 1.5 1 801 1234 131 1501 1.5 1 465 1036 132 1397 1.5 1 473 924 133 1246 1.5 1 452 794 134 1181 1.5 1 412 769 135 1127 1.5 1 390 737 136 1038 1.5 1 304 734 137 1045 1.5 1 343 702 138 904 1.5 1 287 617 139 758 1.5 1 271 487 140 666 1.5 1 277 389 141 539 1.5 1 308 231 142 495 1.5 1 326 169 143 286 1.5 1 201 85 144 666 1.5 1 577 89 145 611 1.5 1 538 73 146 810 1.5 1 733 77 147 816 1.5 1 759 57 148 345 1.5 1 310 35 149 12834 1.5 1 12698 136 150 2376 1.5 1 2316 60 151 81082 1.5 1 80159 923 RUN STATISTICS FOR INPUT FILE: LCo_BSr2_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): 163715 (0.16%)