SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245588_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: 4018). 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 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 SRR18245588_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3589.965 s (50.714 µs/read; 1.18 M reads/minute). === Summary === Total reads processed: 70,788,501 Reads with adapters: 36,934,608 (52.2%) Reads written (passing filters): 70,788,501 (100.0%) Total basepairs processed: 10,618,275,150 bp Quality-trimmed: 29,591,245 bp (0.3%) Total written (filtered): 10,526,842,218 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36934608 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.7% C: 16.6% G: 0.4% T: 30.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 36473191 17697125.2 0 36473191 2 37317 4424281.3 0 37317 3 42493 1106070.3 0 42493 4 17128 276517.6 0 17128 5 8920 69129.4 0 8920 6 7010 17282.3 0 7010 7 6965 4320.6 0 6965 8 7226 1080.1 0 7226 9 6430 270.0 0 6426 4 10 6461 67.5 1 6164 297 11 6435 16.9 1 5899 536 12 6417 4.2 1 6051 366 13 5612 1.1 1 5273 339 14 5849 1.1 1 5498 351 15 5395 1.1 1 5059 336 16 4985 1.1 1 4732 253 17 5770 1.1 1 5416 354 18 4345 1.1 1 4110 235 19 5771 1.1 1 5436 335 20 4330 1.1 1 4098 232 21 3929 1.1 1 3673 256 22 4173 1.1 1 3969 204 23 4186 1.1 1 3955 231 24 4841 1.1 1 4556 285 25 4114 1.1 1 3930 184 26 3458 1.1 1 3258 200 27 3672 1.1 1 3396 276 28 3635 1.1 1 3474 161 29 3215 1.1 1 3024 191 30 3387 1.1 1 3223 164 31 3266 1.1 1 3124 142 32 2998 1.1 1 2873 125 33 3385 1.1 1 3202 183 34 3164 1.1 1 2947 217 35 2721 1.1 1 2588 133 36 2865 1.1 1 2598 267 37 3219 1.1 1 3085 134 38 2130 1.1 1 1978 152 39 2905 1.1 1 2764 141 40 1961 1.1 1 1826 135 41 2349 1.1 1 2239 110 42 3295 1.1 1 3117 178 43 1725 1.1 1 1578 147 44 6575 1.1 1 6289 286 45 3269 1.1 1 3113 156 46 940 1.1 1 884 56 47 3122 1.1 1 3031 91 48 1262 1.1 1 1205 57 49 1095 1.1 1 1038 57 50 1053 1.1 1 1014 39 51 814 1.1 1 769 45 52 709 1.1 1 679 30 53 1422 1.1 1 1379 43 54 2247 1.1 1 2167 80 55 1008 1.1 1 965 43 56 1465 1.1 1 1412 53 57 2908 1.1 1 2840 68 58 1284 1.1 1 1220 64 59 1156 1.1 1 1111 45 60 2038 1.1 1 1989 49 61 1405 1.1 1 1356 49 62 985 1.1 1 947 38 63 2070 1.1 1 2017 53 64 2983 1.1 1 2920 63 65 2108 1.1 1 2068 40 66 1726 1.1 1 1688 38 67 2375 1.1 1 2338 37 68 1053 1.1 1 1021 32 69 1092 1.1 1 1068 24 70 1044 1.1 1 1024 20 71 532 1.1 1 516 16 72 349 1.1 1 320 29 73 276 1.1 1 257 19 74 269 1.1 1 257 12 75 324 1.1 1 304 20 76 548 1.1 1 524 24 77 546 1.1 1 524 22 78 681 1.1 1 661 20 79 797 1.1 1 774 23 80 899 1.1 1 874 25 81 848 1.1 1 824 24 82 954 1.1 1 927 27 83 1079 1.1 1 1039 40 84 964 1.1 1 934 30 85 1032 1.1 1 1007 25 86 966 1.1 1 920 46 87 886 1.1 1 853 33 88 888 1.1 1 863 25 89 871 1.1 1 843 28 90 900 1.1 1 868 32 91 849 1.1 1 822 27 92 823 1.1 1 807 16 93 859 1.1 1 835 24 94 838 1.1 1 802 36 95 764 1.1 1 738 26 96 776 1.1 1 751 25 97 804 1.1 1 781 23 98 812 1.1 1 778 34 99 826 1.1 1 801 25 100 890 1.1 1 859 31 101 745 1.1 1 727 18 102 782 1.1 1 762 20 103 724 1.1 1 701 23 104 727 1.1 1 696 31 105 743 1.1 1 712 31 106 701 1.1 1 681 20 107 736 1.1 1 705 31 108 633 1.1 1 614 19 109 659 1.1 1 631 28 110 652 1.1 1 625 27 111 604 1.1 1 576 28 112 545 1.1 1 525 20 113 602 1.1 1 562 40 114 578 1.1 1 559 19 115 606 1.1 1 550 56 116 599 1.1 1 557 42 117 552 1.1 1 498 54 118 545 1.1 1 481 64 119 599 1.1 1 509 90 120 610 1.1 1 464 146 121 635 1.1 1 421 214 122 741 1.1 1 456 285 123 928 1.1 1 517 411 124 927 1.1 1 418 509 125 1122 1.1 1 450 672 126 1254 1.1 1 446 808 127 1410 1.1 1 415 995 128 1458 1.1 1 415 1043 129 1437 1.1 1 469 968 130 1313 1.1 1 420 893 131 1088 1.1 1 414 674 132 1046 1.1 1 496 550 133 936 1.1 1 501 435 134 921 1.1 1 512 409 135 887 1.1 1 450 437 136 912 1.1 1 503 409 137 839 1.1 1 468 371 138 900 1.1 1 571 329 139 850 1.1 1 614 236 140 997 1.1 1 777 220 141 1422 1.1 1 1270 152 142 1565 1.1 1 1462 103 143 1937 1.1 1 1831 106 144 2720 1.1 1 2618 102 145 4922 1.1 1 4814 108 146 3140 1.1 1 3035 105 147 859 1.1 1 821 38 148 14865 1.1 1 14736 129 149 5348 1.1 1 5282 66 150 49586 1.1 1 49121 465 RUN STATISTICS FOR INPUT FILE: SRR18245588_2.fastq.gz ============================================= 70788501 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 70788501 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 109761 (0.16%)