SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245599_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 40595). 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 Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245599_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4472.285 s (54.061 µs/read; 1.11 M reads/minute). === Summary === Total reads processed: 82,727,298 Reads with adapters: 43,633,185 (52.7%) Reads written (passing filters): 82,727,298 (100.0%) Total basepairs processed: 12,409,094,700 bp Quality-trimmed: 29,402,490 bp (0.2%) Total written (filtered): 12,165,944,309 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43633185 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.9% C: 19.7% G: 0.4% T: 30.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 38507851 20681824.5 0 38507851 2 194342 5170456.1 0 194342 3 191460 1292614.0 0 191460 4 166248 323153.5 0 166248 5 148482 80788.4 0 148482 6 135675 20197.1 0 135675 7 137479 5049.3 0 137479 8 143256 1262.3 0 143256 9 109673 315.6 0 109178 495 10 129274 78.9 1 121124 8150 11 120366 19.7 1 111012 9354 12 121666 4.9 1 112228 9438 13 110095 1.2 1 102365 7730 14 116082 1.2 1 106856 9226 15 100240 1.2 1 93166 7074 16 101425 1.2 1 93591 7834 17 114699 1.2 1 106529 8170 18 77365 1.2 1 72070 5295 19 99801 1.2 1 92445 7356 20 93897 1.2 1 87452 6445 21 72684 1.2 1 67403 5281 22 80900 1.2 1 75596 5304 23 77051 1.2 1 71952 5099 24 90415 1.2 1 83944 6471 25 81311 1.2 1 76344 4967 26 58148 1.2 1 53983 4165 27 60410 1.2 1 55856 4554 28 67440 1.2 1 63450 3990 29 59464 1.2 1 55305 4159 30 62737 1.2 1 58744 3993 31 54742 1.2 1 51245 3497 32 55488 1.2 1 52119 3369 33 62453 1.2 1 58200 4253 34 49114 1.2 1 45549 3565 35 47786 1.2 1 44849 2937 36 53268 1.2 1 50187 3081 37 44202 1.2 1 41554 2648 38 42640 1.2 1 40201 2439 39 46247 1.2 1 43591 2656 40 35810 1.2 1 33766 2044 41 40376 1.2 1 38098 2278 42 55591 1.2 1 52752 2839 43 25042 1.2 1 23036 2006 44 64118 1.2 1 60974 3144 45 45574 1.2 1 42983 2591 46 25178 1.2 1 22694 2484 47 73775 1.2 1 71557 2218 48 8808 1.2 1 7805 1003 49 27852 1.2 1 26397 1455 50 10301 1.2 1 9633 668 51 16088 1.2 1 15121 967 52 10536 1.2 1 9751 785 53 26442 1.2 1 25024 1418 54 41065 1.2 1 39505 1560 55 10414 1.2 1 9508 906 56 26312 1.2 1 24347 1965 57 87911 1.2 1 85419 2492 58 15259 1.2 1 14207 1052 59 8072 1.2 1 7097 975 60 54614 1.2 1 52912 1702 61 10066 1.2 1 9421 645 62 7237 1.2 1 6347 890 63 47345 1.2 1 45409 1936 64 59393 1.2 1 57811 1582 65 5206 1.2 1 4671 535 66 11939 1.2 1 11351 588 67 7840 1.2 1 7486 354 68 4329 1.2 1 3935 394 69 7406 1.2 1 6969 437 70 11184 1.2 1 10751 433 71 4042 1.2 1 3760 282 72 4158 1.2 1 3887 271 73 5108 1.2 1 4812 296 74 5394 1.2 1 5056 338 75 8189 1.2 1 7712 477 76 10427 1.2 1 9926 501 77 10854 1.2 1 10344 510 78 11741 1.2 1 11191 550 79 12134 1.2 1 11600 534 80 11806 1.2 1 11270 536 81 11894 1.2 1 11357 537 82 11980 1.2 1 11407 573 83 12687 1.2 1 12122 565 84 12248 1.2 1 11687 561 85 13162 1.2 1 12568 594 86 12086 1.2 1 11548 538 87 10996 1.2 1 10452 544 88 10660 1.2 1 10172 488 89 10576 1.2 1 10063 513 90 10344 1.2 1 9903 441 91 9995 1.2 1 9589 406 92 10064 1.2 1 9647 417 93 9790 1.2 1 9346 444 94 9459 1.2 1 9030 429 95 9259 1.2 1 8861 398 96 9359 1.2 1 8988 371 97 9244 1.2 1 8884 360 98 9449 1.2 1 9031 418 99 9685 1.2 1 9275 410 100 9582 1.2 1 9226 356 101 9029 1.2 1 8638 391 102 8548 1.2 1 8169 379 103 8483 1.2 1 8125 358 104 8164 1.2 1 7783 381 105 8298 1.2 1 7957 341 106 8197 1.2 1 7879 318 107 8207 1.2 1 7862 345 108 8220 1.2 1 7870 350 109 7780 1.2 1 7461 319 110 7841 1.2 1 7503 338 111 7947 1.2 1 7622 325 112 7800 1.2 1 7485 315 113 7938 1.2 1 7640 298 114 7760 1.2 1 7417 343 115 7714 1.2 1 7424 290 116 7548 1.2 1 7255 293 117 7426 1.2 1 7110 316 118 7692 1.2 1 7353 339 119 7518 1.2 1 7157 361 120 7577 1.2 1 7170 407 121 7591 1.2 1 7150 441 122 7315 1.2 1 6774 541 123 7986 1.2 1 7233 753 124 7714 1.2 1 6862 852 125 7728 1.2 1 6663 1065 126 7527 1.2 1 6235 1292 127 7380 1.2 1 5940 1440 128 7449 1.2 1 5731 1718 129 7386 1.2 1 5413 1973 130 6946 1.2 1 4779 2167 131 7335 1.2 1 4713 2622 132 7461 1.2 1 4382 3079 133 7751 1.2 1 4128 3623 134 7260 1.2 1 3597 3663 135 6840 1.2 1 3264 3576 136 6120 1.2 1 2821 3299 137 5037 1.2 1 2567 2470 138 4385 1.2 1 2711 1674 139 3943 1.2 1 2672 1271 140 3737 1.2 1 2715 1022 141 3901 1.2 1 3179 722 142 3088 1.2 1 2610 478 143 3234 1.2 1 2735 499 144 4168 1.2 1 3524 644 145 5383 1.2 1 4574 809 146 2869 1.2 1 2301 568 147 435 1.2 1 278 157 148 5011 1.2 1 4281 730 149 2105 1.2 1 1715 390 150 45082 1.2 1 39488 5594 RUN STATISTICS FOR INPUT FILE: SRR18245599_2.fastq.gz ============================================= 82727298 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82727298 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 157191 (0.19%)