SUMMARISING RUN PARAMETERS ========================== Input filename: LCo_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: 5205). 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_BSr1_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 472.699 s (4.727 µs/read; 12.69 M reads/minute). === Summary === Total reads processed: 100,000,000 Reads with adapters: 43,499,149 (43.5%) Reads written (passing filters): 100,000,000 (100.0%) Total basepairs processed: 15,100,000,000 bp Quality-trimmed: 11,505,102 bp (0.1%) Total written (filtered): 15,006,496,282 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43499149 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.9% C: 1.9% G: 11.3% T: 44.7% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 35097596 25000000.0 0 35097596 2 4809560 6250000.0 0 4809560 3 1992154 1562500.0 0 1992154 4 807258 390625.0 0 807258 5 46954 97656.2 0 46954 6 43451 24414.1 0 43451 7 35626 6103.5 0 35626 8 40454 1525.9 0 40454 9 29846 381.5 0 29172 674 10 31258 95.4 1 29179 2079 11 31940 23.8 1 29496 2444 12 28831 6.0 1 27302 1529 13 26184 1.5 1 25030 1154 14 23593 1.5 1 22070 1523 15 24721 1.5 1 23518 1203 16 19185 1.5 1 17976 1209 17 21596 1.5 1 20068 1528 18 24478 1.5 1 23450 1028 19 9428 1.5 1 8946 482 20 16584 1.5 1 15751 833 21 15258 1.5 1 14487 771 22 13155 1.5 1 12629 526 23 14844 1.5 1 14047 797 24 11252 1.5 1 10438 814 25 12561 1.5 1 12016 545 26 8698 1.5 1 8326 372 27 10259 1.5 1 9713 546 28 9386 1.5 1 8991 395 29 8701 1.5 1 8120 581 30 9621 1.5 1 9244 377 31 5110 1.5 1 4863 247 32 7481 1.5 1 7183 298 33 6137 1.5 1 5806 331 34 6303 1.5 1 6031 272 35 7548 1.5 1 7108 440 36 3574 1.5 1 3408 166 37 5135 1.5 1 4888 247 38 5070 1.5 1 4834 236 39 4367 1.5 1 4243 124 40 4607 1.5 1 4398 209 41 4100 1.5 1 3877 223 42 3164 1.5 1 3052 112 43 4049 1.5 1 3777 272 44 2859 1.5 1 2714 145 45 5080 1.5 1 4927 153 46 826 1.5 1 776 50 47 2676 1.5 1 2558 118 48 3024 1.5 1 2907 117 49 2124 1.5 1 2055 69 50 2369 1.5 1 2257 112 51 2203 1.5 1 2071 132 52 2107 1.5 1 2026 81 53 2022 1.5 1 1944 78 54 1935 1.5 1 1841 94 55 2415 1.5 1 2320 95 56 1117 1.5 1 1070 47 57 1827 1.5 1 1768 59 58 2114 1.5 1 2023 91 59 737 1.5 1 692 45 60 1565 1.5 1 1535 30 61 957 1.5 1 911 46 62 1366 1.5 1 1299 67 63 1474 1.5 1 1423 51 64 1250 1.5 1 1207 43 65 664 1.5 1 637 27 66 1125 1.5 1 1084 41 67 1288 1.5 1 1260 28 68 1479 1.5 1 1420 59 69 1049 1.5 1 1004 45 70 1421 1.5 1 1354 67 71 132 1.5 1 123 9 72 218 1.5 1 210 8 73 525 1.5 1 506 19 74 685 1.5 1 658 27 75 640 1.5 1 616 24 76 693 1.5 1 666 27 77 666 1.5 1 599 67 78 923 1.5 1 742 181 79 715 1.5 1 620 95 80 615 1.5 1 563 52 81 574 1.5 1 543 31 82 551 1.5 1 532 19 83 494 1.5 1 478 16 84 498 1.5 1 471 27 85 461 1.5 1 442 19 86 458 1.5 1 441 17 87 425 1.5 1 409 16 88 440 1.5 1 424 16 89 417 1.5 1 406 11 90 369 1.5 1 355 14 91 378 1.5 1 357 21 92 357 1.5 1 341 16 93 373 1.5 1 363 10 94 324 1.5 1 313 11 95 333 1.5 1 318 15 96 318 1.5 1 310 8 97 327 1.5 1 318 9 98 335 1.5 1 317 18 99 273 1.5 1 263 10 100 260 1.5 1 246 14 101 289 1.5 1 280 9 102 276 1.5 1 269 7 103 283 1.5 1 274 9 104 318 1.5 1 312 6 105 251 1.5 1 246 5 106 258 1.5 1 248 10 107 224 1.5 1 215 9 108 224 1.5 1 215 9 109 214 1.5 1 202 12 110 211 1.5 1 204 7 111 199 1.5 1 191 8 112 204 1.5 1 191 13 113 226 1.5 1 216 10 114 239 1.5 1 230 9 115 254 1.5 1 245 9 116 276 1.5 1 265 11 117 273 1.5 1 264 9 118 285 1.5 1 277 8 119 369 1.5 1 362 7 120 400 1.5 1 392 8 121 450 1.5 1 438 12 122 533 1.5 1 521 12 123 583 1.5 1 569 14 124 610 1.5 1 595 15 125 561 1.5 1 547 14 126 551 1.5 1 547 4 127 451 1.5 1 446 5 128 346 1.5 1 337 9 129 356 1.5 1 353 3 130 261 1.5 1 257 4 131 180 1.5 1 178 2 132 247 1.5 1 240 7 133 209 1.5 1 204 5 134 224 1.5 1 217 7 135 201 1.5 1 191 10 136 161 1.5 1 159 2 137 171 1.5 1 164 7 138 183 1.5 1 169 14 139 216 1.5 1 203 13 140 172 1.5 1 167 5 141 178 1.5 1 174 4 142 228 1.5 1 222 6 143 149 1.5 1 145 4 144 384 1.5 1 366 18 145 386 1.5 1 368 18 146 506 1.5 1 485 21 147 562 1.5 1 525 37 148 363 1.5 1 331 32 149 10469 1.5 1 10074 395 150 2463 1.5 1 2282 181 151 67595 1.5 1 62763 4832 RUN STATISTICS FOR INPUT FILE: LCo_BSr1_1.fastq.gz ============================================= 100000000 sequences processed in total