SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_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: 4945). 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 LYa_BSr2_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 447.282 s (4.473 µs/read; 13.41 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 46,681,642 (46.7%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 33,150,714 bp (0.2%) Total written (filtered): 14,989,738,068 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46681642 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.3% C: 17.1% G: 0.4% T: 33.1% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 45859698 25000000.0 0 45859698 2 81117 6250000.0 0 81117 3 52092 1562500.0 0 52092 4 35339 390625.0 0 35339 5 32934 97656.2 0 32934 6 27328 24414.1 0 27328 7 24514 6103.5 0 24514 8 27922 1525.9 0 27922 9 15166 381.5 0 15137 29 10 23468 95.4 1 19721 3747 11 19260 23.8 1 16017 3243 12 20411 6.0 1 17203 3208 13 19079 1.5 1 16019 3060 14 20249 1.5 1 16918 3331 15 13702 1.5 1 11738 1964 16 15294 1.5 1 12966 2328 17 19180 1.5 1 16477 2703 18 8231 1.5 1 6911 1320 19 16578 1.5 1 14319 2259 20 12853 1.5 1 11166 1687 21 6215 1.5 1 5376 839 22 10351 1.5 1 8940 1411 23 10114 1.5 1 8775 1339 24 12482 1.5 1 10778 1704 25 10727 1.5 1 9464 1263 26 6435 1.5 1 5517 918 27 4464 1.5 1 3786 678 28 8658 1.5 1 7676 982 29 5267 1.5 1 4661 606 30 8063 1.5 1 7271 792 31 4367 1.5 1 3857 510 32 7136 1.5 1 6387 749 33 3970 1.5 1 3517 453 34 5620 1.5 1 5087 533 35 4372 1.5 1 3980 392 36 4488 1.5 1 3987 501 37 4341 1.5 1 3920 421 38 4694 1.5 1 4274 420 39 3185 1.5 1 2872 313 40 4166 1.5 1 3853 313 41 2869 1.5 1 2624 245 42 3624 1.5 1 3323 301 43 2884 1.5 1 2625 259 44 2920 1.5 1 2682 238 45 3199 1.5 1 2921 278 46 2786 1.5 1 2536 250 47 2406 1.5 1 2261 145 48 2415 1.5 1 2245 170 49 2303 1.5 1 2092 211 50 2270 1.5 1 2120 150 51 2047 1.5 1 1887 160 52 2120 1.5 1 1949 171 53 2000 1.5 1 1855 145 54 2266 1.5 1 2112 154 55 1398 1.5 1 1311 87 56 1841 1.5 1 1701 140 57 2005 1.5 1 1884 121 58 1282 1.5 1 1194 88 59 1549 1.5 1 1468 81 60 1511 1.5 1 1431 80 61 1449 1.5 1 1371 78 62 1311 1.5 1 1233 78 63 2274 1.5 1 2161 113 64 1112 1.5 1 1048 64 65 956 1.5 1 897 59 66 808 1.5 1 759 49 67 1358 1.5 1 1307 51 68 1130 1.5 1 1061 69 69 983 1.5 1 926 57 70 1120 1.5 1 1065 55 71 1084 1.5 1 1014 70 72 1131 1.5 1 1072 59 73 1451 1.5 1 1380 71 74 1045 1.5 1 974 71 75 707 1.5 1 628 79 76 445 1.5 1 397 48 77 740 1.5 1 684 56 78 859 1.5 1 694 165 79 849 1.5 1 748 101 80 797 1.5 1 731 66 81 747 1.5 1 696 51 82 711 1.5 1 672 39 83 665 1.5 1 620 45 84 726 1.5 1 689 37 85 763 1.5 1 721 42 86 659 1.5 1 633 26 87 598 1.5 1 569 29 88 526 1.5 1 501 25 89 539 1.5 1 514 25 90 545 1.5 1 525 20 91 512 1.5 1 484 28 92 529 1.5 1 504 25 93 460 1.5 1 439 21 94 485 1.5 1 463 22 95 457 1.5 1 439 18 96 440 1.5 1 426 14 97 447 1.5 1 428 19 98 462 1.5 1 440 22 99 405 1.5 1 390 15 100 409 1.5 1 391 18 101 375 1.5 1 357 18 102 369 1.5 1 351 18 103 363 1.5 1 345 18 104 466 1.5 1 448 18 105 372 1.5 1 354 18 106 375 1.5 1 353 22 107 330 1.5 1 304 26 108 353 1.5 1 328 25 109 307 1.5 1 285 22 110 296 1.5 1 271 25 111 301 1.5 1 274 27 112 304 1.5 1 276 28 113 301 1.5 1 277 24 114 305 1.5 1 285 20 115 355 1.5 1 320 35 116 291 1.5 1 254 37 117 324 1.5 1 282 42 118 341 1.5 1 279 62 119 375 1.5 1 300 75 120 404 1.5 1 307 97 121 456 1.5 1 302 154 122 646 1.5 1 388 258 123 810 1.5 1 439 371 124 1240 1.5 1 728 512 125 1153 1.5 1 432 721 126 1261 1.5 1 418 843 127 1382 1.5 1 386 996 128 1672 1.5 1 459 1213 129 1723 1.5 1 392 1331 130 1956 1.5 1 682 1274 131 1553 1.5 1 425 1128 132 1395 1.5 1 442 953 133 1249 1.5 1 490 759 134 1105 1.5 1 393 712 135 1071 1.5 1 384 687 136 1109 1.5 1 330 779 137 1074 1.5 1 349 725 138 965 1.5 1 309 656 139 812 1.5 1 282 530 140 689 1.5 1 280 409 141 559 1.5 1 304 255 142 502 1.5 1 347 155 143 327 1.5 1 231 96 144 614 1.5 1 523 91 145 699 1.5 1 586 113 146 976 1.5 1 883 93 147 897 1.5 1 842 55 148 374 1.5 1 346 28 149 14240 1.5 1 14075 165 150 2290 1.5 1 2226 64 151 78017 1.5 1 77164 853 RUN STATISTICS FOR INPUT FILE: LYa_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): 165956 (0.17%)