SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245587_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: 4659). 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 SRR18245587_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3691.390 s (54.749 µs/read; 1.10 M reads/minute). === Summary === Total reads processed: 67,423,445 Reads with adapters: 34,868,914 (51.7%) Reads written (passing filters): 67,423,445 (100.0%) Total basepairs processed: 10,113,516,750 bp Quality-trimmed: 28,067,935 bp (0.3%) Total written (filtered): 10,021,715,408 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34868914 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.5% C: 16.9% G: 0.4% T: 30.0% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 34373073 16855861.2 0 34373073 2 40443 4213965.3 0 40443 3 54133 1053491.3 0 54133 4 17750 263372.8 0 17750 5 9131 65843.2 0 9131 6 6357 16460.8 0 6357 7 6494 4115.2 0 6494 8 6677 1028.8 0 6677 9 5623 257.2 0 5614 9 10 6242 64.3 1 5961 281 11 5962 16.1 1 5445 517 12 5964 4.0 1 5588 376 13 5197 1.0 1 4897 300 14 5721 1.0 1 5360 361 15 4844 1.0 1 4587 257 16 4775 1.0 1 4541 234 17 5650 1.0 1 5334 316 18 3555 1.0 1 3361 194 19 5498 1.0 1 5169 329 20 3771 1.0 1 3575 196 21 3576 1.0 1 3362 214 22 3853 1.0 1 3682 171 23 3725 1.0 1 3543 182 24 4590 1.0 1 4290 300 25 4003 1.0 1 3788 215 26 3179 1.0 1 2981 198 27 3032 1.0 1 2819 213 28 3559 1.0 1 3424 135 29 3065 1.0 1 2866 199 30 3365 1.0 1 3188 177 31 2825 1.0 1 2656 169 32 2918 1.0 1 2807 111 33 3139 1.0 1 2884 255 34 3476 1.0 1 3286 190 35 2092 1.0 1 1928 164 36 3221 1.0 1 3049 172 37 2910 1.0 1 2771 139 38 3412 1.0 1 3188 224 39 1403 1.0 1 1330 73 40 2090 1.0 1 1968 122 41 2092 1.0 1 1996 96 42 3502 1.0 1 3329 173 43 1715 1.0 1 1628 87 44 8821 1.0 1 8611 210 45 2719 1.0 1 2582 137 46 651 1.0 1 602 49 47 2626 1.0 1 2548 78 48 806 1.0 1 766 40 49 1075 1.0 1 1029 46 50 589 1.0 1 546 43 51 716 1.0 1 677 39 52 367 1.0 1 339 28 53 1456 1.0 1 1419 37 54 2410 1.0 1 2326 84 55 887 1.0 1 841 46 56 1436 1.0 1 1394 42 57 2946 1.0 1 2885 61 58 1061 1.0 1 1017 44 59 1143 1.0 1 1113 30 60 2851 1.0 1 2789 62 61 1785 1.0 1 1744 41 62 559 1.0 1 527 32 63 2304 1.0 1 2240 64 64 4967 1.0 1 4882 85 65 2230 1.0 1 2184 46 66 1823 1.0 1 1775 48 67 1670 1.0 1 1628 42 68 568 1.0 1 534 34 69 589 1.0 1 575 14 70 722 1.0 1 704 18 71 349 1.0 1 324 25 72 276 1.0 1 254 22 73 274 1.0 1 259 15 74 296 1.0 1 271 25 75 409 1.0 1 378 31 76 662 1.0 1 643 19 77 666 1.0 1 641 25 78 775 1.0 1 749 26 79 910 1.0 1 877 33 80 980 1.0 1 955 25 81 1015 1.0 1 985 30 82 907 1.0 1 889 18 83 1131 1.0 1 1104 27 84 1090 1.0 1 1045 45 85 1188 1.0 1 1151 37 86 1128 1.0 1 1096 32 87 993 1.0 1 969 24 88 904 1.0 1 878 26 89 934 1.0 1 902 32 90 996 1.0 1 961 35 91 890 1.0 1 863 27 92 909 1.0 1 882 27 93 910 1.0 1 892 18 94 848 1.0 1 815 33 95 935 1.0 1 903 32 96 814 1.0 1 792 22 97 872 1.0 1 839 33 98 903 1.0 1 881 22 99 852 1.0 1 836 16 100 908 1.0 1 880 28 101 830 1.0 1 805 25 102 794 1.0 1 771 23 103 789 1.0 1 765 24 104 746 1.0 1 718 28 105 685 1.0 1 667 18 106 738 1.0 1 720 18 107 752 1.0 1 733 19 108 757 1.0 1 725 32 109 713 1.0 1 687 26 110 607 1.0 1 590 17 111 660 1.0 1 636 24 112 635 1.0 1 611 24 113 608 1.0 1 586 22 114 632 1.0 1 611 21 115 587 1.0 1 563 24 116 585 1.0 1 550 35 117 582 1.0 1 530 52 118 583 1.0 1 523 60 119 597 1.0 1 491 106 120 773 1.0 1 591 182 121 759 1.0 1 520 239 122 846 1.0 1 514 332 123 1068 1.0 1 703 365 124 987 1.0 1 481 506 125 1193 1.0 1 537 656 126 1310 1.0 1 548 762 127 1356 1.0 1 443 913 128 1336 1.0 1 451 885 129 1533 1.0 1 542 991 130 1327 1.0 1 514 813 131 1254 1.0 1 541 713 132 1098 1.0 1 532 566 133 1080 1.0 1 531 549 134 1041 1.0 1 525 516 135 1057 1.0 1 510 547 136 1098 1.0 1 542 556 137 1013 1.0 1 552 461 138 1053 1.0 1 647 406 139 1110 1.0 1 787 323 140 1188 1.0 1 949 239 141 1609 1.0 1 1412 197 142 1713 1.0 1 1606 107 143 2257 1.0 1 2119 138 144 2998 1.0 1 2877 121 145 5280 1.0 1 5155 125 146 3324 1.0 1 3221 103 147 1139 1.0 1 1087 52 148 20187 1.0 1 19988 199 149 7522 1.0 1 7433 89 150 64422 1.0 1 63756 666 RUN STATISTICS FOR INPUT FILE: SRR18245587_2.fastq.gz ============================================= 67423445 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 67423445 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 138040 (0.20%)