SUMMARISING RUN PARAMETERS ========================== Input filename: LYa_BSr1_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: 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_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 421.945 s (4.219 µs/read; 14.22 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,217,107 (43.2%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 11,308,331 bp (0.1%) Total written (filtered): 15,012,372,708 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43217107 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.0% C: 1.1% G: 11.4% T: 45.4% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 35106688 25000000.0 0 35106688 2 4866992 6250000.0 0 4866992 3 1975391 1562500.0 0 1975391 4 795902 390625.0 0 795902 5 23870 97656.2 0 23870 6 21941 24414.1 0 21941 7 17263 6103.5 0 17263 8 19043 1525.9 0 19043 9 15550 381.5 0 14861 689 10 15818 95.4 1 14283 1535 11 15798 23.8 1 14409 1389 12 14222 6.0 1 13471 751 13 12179 1.5 1 11623 556 14 12355 1.5 1 11546 809 15 11403 1.5 1 10822 581 16 10120 1.5 1 9469 651 17 11110 1.5 1 10337 773 18 12047 1.5 1 11539 508 19 5203 1.5 1 4934 269 20 8144 1.5 1 7760 384 21 8132 1.5 1 7713 419 22 6873 1.5 1 6612 261 23 7641 1.5 1 7218 423 24 6588 1.5 1 6121 467 25 6487 1.5 1 6191 296 26 4933 1.5 1 4698 235 27 5756 1.5 1 5421 335 28 5501 1.5 1 5251 250 29 4991 1.5 1 4669 322 30 5691 1.5 1 5447 244 31 3141 1.5 1 3018 123 32 4521 1.5 1 4323 198 33 3644 1.5 1 3436 208 34 3938 1.5 1 3726 212 35 4259 1.5 1 4049 210 36 2452 1.5 1 2334 118 37 3338 1.5 1 3137 201 38 3540 1.5 1 3384 156 39 2688 1.5 1 2508 180 40 3336 1.5 1 3198 138 41 2242 1.5 1 2152 90 42 2181 1.5 1 2095 86 43 2594 1.5 1 2420 174 44 1912 1.5 1 1803 109 45 3499 1.5 1 3394 105 46 592 1.5 1 546 46 47 1795 1.5 1 1719 76 48 2226 1.5 1 2143 83 49 1505 1.5 1 1444 61 50 1733 1.5 1 1647 86 51 1624 1.5 1 1521 103 52 1524 1.5 1 1445 79 53 1420 1.5 1 1358 62 54 1481 1.5 1 1402 79 55 1915 1.5 1 1817 98 56 769 1.5 1 721 48 57 1508 1.5 1 1437 71 58 1529 1.5 1 1473 56 59 654 1.5 1 607 47 60 1211 1.5 1 1181 30 61 588 1.5 1 551 37 62 1056 1.5 1 1007 49 63 1227 1.5 1 1181 46 64 864 1.5 1 833 31 65 477 1.5 1 454 23 66 961 1.5 1 918 43 67 1065 1.5 1 1017 48 68 1135 1.5 1 1101 34 69 867 1.5 1 813 54 70 1063 1.5 1 1007 56 71 104 1.5 1 89 15 72 171 1.5 1 158 13 73 443 1.5 1 426 17 74 556 1.5 1 530 26 75 543 1.5 1 518 25 76 580 1.5 1 551 29 77 545 1.5 1 485 60 78 720 1.5 1 587 133 79 643 1.5 1 546 97 80 546 1.5 1 502 44 81 519 1.5 1 494 25 82 466 1.5 1 441 25 83 415 1.5 1 381 34 84 448 1.5 1 417 31 85 413 1.5 1 390 23 86 413 1.5 1 386 27 87 389 1.5 1 372 17 88 351 1.5 1 322 29 89 338 1.5 1 322 16 90 328 1.5 1 310 18 91 336 1.5 1 316 20 92 314 1.5 1 293 21 93 273 1.5 1 262 11 94 303 1.5 1 289 14 95 284 1.5 1 269 15 96 280 1.5 1 262 18 97 266 1.5 1 257 9 98 277 1.5 1 258 19 99 245 1.5 1 227 18 100 254 1.5 1 244 10 101 252 1.5 1 233 19 102 253 1.5 1 246 7 103 228 1.5 1 218 10 104 291 1.5 1 279 12 105 224 1.5 1 214 10 106 221 1.5 1 212 9 107 219 1.5 1 205 14 108 194 1.5 1 183 11 109 170 1.5 1 165 5 110 179 1.5 1 170 9 111 175 1.5 1 165 10 112 174 1.5 1 166 8 113 179 1.5 1 170 9 114 194 1.5 1 184 10 115 205 1.5 1 193 12 116 248 1.5 1 234 14 117 219 1.5 1 213 6 118 221 1.5 1 212 9 119 277 1.5 1 268 9 120 333 1.5 1 325 8 121 325 1.5 1 318 7 122 373 1.5 1 366 7 123 434 1.5 1 430 4 124 441 1.5 1 431 10 125 417 1.5 1 409 8 126 403 1.5 1 395 8 127 331 1.5 1 327 4 128 301 1.5 1 294 7 129 266 1.5 1 261 5 130 215 1.5 1 208 7 131 166 1.5 1 164 2 132 191 1.5 1 183 8 133 193 1.5 1 185 8 134 190 1.5 1 184 6 135 182 1.5 1 176 6 136 177 1.5 1 171 6 137 142 1.5 1 136 6 138 192 1.5 1 183 9 139 186 1.5 1 175 11 140 172 1.5 1 160 12 141 165 1.5 1 156 9 142 200 1.5 1 188 12 143 127 1.5 1 118 9 144 374 1.5 1 348 26 145 367 1.5 1 351 16 146 415 1.5 1 382 33 147 454 1.5 1 429 25 148 345 1.5 1 316 29 149 10396 1.5 1 10007 389 150 2482 1.5 1 2313 169 151 68560 1.5 1 63667 4893 RUN STATISTICS FOR INPUT FILE: LYa_BSr1_1.fastq.gz ============================================= 100000000 sequences processed in total