SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_BSr1_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: 3253). 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 LYa_BSr1_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 420.408 s (4.204 µs/read; 14.27 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 46,771,633 (46.8%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 31,210,713 bp (0.2%) Total written (filtered): 15,000,008,668 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46771633 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.6% C: 17.0% G: 0.3% T: 33.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 46200304 25000000.0 0 46200304 2 67646 6250000.0 0 67646 3 38764 1562500.0 0 38764 4 24996 390625.0 0 24996 5 21297 97656.2 0 21297 6 17216 24414.1 0 17216 7 15503 6103.5 0 15503 8 17877 1525.9 0 17877 9 8546 381.5 0 8526 20 10 15503 95.4 1 12714 2789 11 11676 23.8 1 9540 2136 12 13050 6.0 1 10626 2424 13 11811 1.5 1 9685 2126 14 13041 1.5 1 10697 2344 15 8498 1.5 1 7062 1436 16 9478 1.5 1 7909 1569 17 12427 1.5 1 10531 1896 18 5199 1.5 1 4319 880 19 10841 1.5 1 9277 1564 20 8128 1.5 1 6954 1174 21 4140 1.5 1 3520 620 22 6937 1.5 1 5922 1015 23 6544 1.5 1 5593 951 24 8296 1.5 1 7009 1287 25 7010 1.5 1 6073 937 26 4241 1.5 1 3579 662 27 2985 1.5 1 2489 496 28 5731 1.5 1 5019 712 29 3799 1.5 1 3338 461 30 5431 1.5 1 4838 593 31 3275 1.5 1 2887 388 32 4106 1.5 1 3599 507 33 4468 1.5 1 3894 574 34 3146 1.5 1 2789 357 35 3553 1.5 1 3161 392 36 2719 1.5 1 2376 343 37 3109 1.5 1 2852 257 38 2698 1.5 1 2376 322 39 3106 1.5 1 2791 315 40 2883 1.5 1 2651 232 41 1902 1.5 1 1652 250 42 2411 1.5 1 2201 210 43 2151 1.5 1 1916 235 44 2001 1.5 1 1800 201 45 2240 1.5 1 2026 214 46 2042 1.5 1 1835 207 47 1657 1.5 1 1532 125 48 1743 1.5 1 1590 153 49 1797 1.5 1 1614 183 50 1562 1.5 1 1445 117 51 1471 1.5 1 1351 120 52 1498 1.5 1 1364 134 53 1381 1.5 1 1270 111 54 1582 1.5 1 1458 124 55 1055 1.5 1 975 80 56 1293 1.5 1 1199 94 57 1575 1.5 1 1464 111 58 779 1.5 1 713 66 59 1009 1.5 1 948 61 60 1107 1.5 1 1044 63 61 1077 1.5 1 1009 68 62 836 1.5 1 782 54 63 1463 1.5 1 1368 95 64 816 1.5 1 777 39 65 682 1.5 1 638 44 66 594 1.5 1 534 60 67 901 1.5 1 849 52 68 757 1.5 1 719 38 69 685 1.5 1 638 47 70 707 1.5 1 667 40 71 713 1.5 1 658 55 72 741 1.5 1 689 52 73 1013 1.5 1 936 77 74 704 1.5 1 648 56 75 481 1.5 1 415 66 76 261 1.5 1 239 22 77 388 1.5 1 360 28 78 541 1.5 1 451 90 79 546 1.5 1 470 76 80 494 1.5 1 447 47 81 492 1.5 1 464 28 82 433 1.5 1 409 24 83 402 1.5 1 371 31 84 441 1.5 1 416 25 85 428 1.5 1 398 30 86 420 1.5 1 393 27 87 375 1.5 1 352 23 88 336 1.5 1 319 17 89 327 1.5 1 307 20 90 318 1.5 1 302 16 91 324 1.5 1 302 22 92 287 1.5 1 271 16 93 275 1.5 1 254 21 94 296 1.5 1 274 22 95 272 1.5 1 253 19 96 258 1.5 1 246 12 97 260 1.5 1 247 13 98 261 1.5 1 243 18 99 231 1.5 1 220 11 100 258 1.5 1 240 18 101 247 1.5 1 233 14 102 226 1.5 1 209 17 103 216 1.5 1 198 18 104 284 1.5 1 266 18 105 213 1.5 1 193 20 106 206 1.5 1 188 18 107 203 1.5 1 183 20 108 174 1.5 1 156 18 109 171 1.5 1 153 18 110 168 1.5 1 146 22 111 165 1.5 1 143 22 112 159 1.5 1 139 20 113 177 1.5 1 148 29 114 171 1.5 1 148 23 115 205 1.5 1 173 32 116 188 1.5 1 167 21 117 199 1.5 1 162 37 118 197 1.5 1 147 50 119 258 1.5 1 176 82 120 294 1.5 1 187 107 121 356 1.5 1 199 157 122 478 1.5 1 236 242 123 613 1.5 1 274 339 124 960 1.5 1 467 493 125 882 1.5 1 257 625 126 1069 1.5 1 276 793 127 1307 1.5 1 256 1051 128 1441 1.5 1 302 1139 129 1645 1.5 1 316 1329 130 1765 1.5 1 552 1213 131 1421 1.5 1 305 1116 132 1207 1.5 1 312 895 133 1060 1.5 1 332 728 134 875 1.5 1 271 604 135 938 1.5 1 321 617 136 895 1.5 1 283 612 137 819 1.5 1 266 553 138 769 1.5 1 254 515 139 630 1.5 1 195 435 140 527 1.5 1 205 322 141 414 1.5 1 196 218 142 306 1.5 1 190 116 143 199 1.5 1 111 88 144 441 1.5 1 348 93 145 436 1.5 1 347 89 146 431 1.5 1 361 70 147 469 1.5 1 401 68 148 288 1.5 1 256 32 149 10147 1.5 1 10041 106 150 1862 1.5 1 1803 59 151 59534 1.5 1 58932 602 RUN STATISTICS FOR INPUT FILE: LYa_BSr1_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): 131655 (0.13%)