SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10683998_1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 249108). 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 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR10683998_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1379.262 s (17.572 µs/read; 3.41 M reads/minute). === Summary === Total reads processed: 78,491,837 Reads with adapters: 52,907,370 (67.4%) Reads written (passing filters): 78,491,837 (100.0%) Total basepairs processed: 11,852,267,387 bp Quality-trimmed: 47,401,879 bp (0.4%) Total written (filtered): 10,894,904,271 bp (91.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 52907370 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.1% C: 19.1% G: 0.9% T: 27.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25382941 19622959.2 0 25382941 2 993825 4905739.8 0 993825 3 699935 1226435.0 0 699935 4 577892 306608.7 0 577892 5 607394 76652.2 0 607394 6 594212 19163.0 0 594212 7 604144 4790.8 0 604144 8 721533 1197.7 0 721533 9 452617 299.4 0 450682 1935 10 608549 74.9 1 538405 70144 11 516352 18.7 1 464708 51644 12 550856 4.7 1 473964 76892 13 517229 1.2 1 445465 71764 14 624171 1.2 1 531868 92303 15 395212 1.2 1 344033 51179 16 506183 1.2 1 442677 63506 17 691976 1.2 1 601959 90017 18 344838 1.2 1 300206 44632 19 665141 1.2 1 577586 87555 20 476866 1.2 1 417290 59576 21 329829 1.2 1 290596 39233 22 435382 1.2 1 382397 52985 23 426120 1.2 1 372195 53925 24 508890 1.2 1 437489 71401 25 475306 1.2 1 417951 57355 26 363046 1.2 1 319698 43348 27 331070 1.2 1 289966 41104 28 467092 1.2 1 410992 56100 29 406948 1.2 1 360649 46299 30 424778 1.2 1 375685 49093 31 414311 1.2 1 366345 47966 32 359231 1.2 1 315036 44195 33 413867 1.2 1 364792 49075 34 269394 1.2 1 240767 28627 35 329183 1.2 1 292000 37183 36 388078 1.2 1 344887 43191 37 263242 1.2 1 234434 28808 38 353671 1.2 1 313887 39784 39 378463 1.2 1 338422 40041 40 288126 1.2 1 259216 28910 41 302176 1.2 1 272089 30087 42 322696 1.2 1 290619 32077 43 239484 1.2 1 215882 23602 44 256979 1.2 1 230513 26466 45 267534 1.2 1 240075 27459 46 257963 1.2 1 232625 25338 47 252364 1.2 1 226533 25831 48 245956 1.2 1 221761 24195 49 274259 1.2 1 247944 26315 50 247368 1.2 1 224256 23112 51 233785 1.2 1 212151 21634 52 227499 1.2 1 206808 20691 53 216601 1.2 1 196198 20403 54 238497 1.2 1 215884 22613 55 163043 1.2 1 148323 14720 56 200160 1.2 1 181454 18706 57 263689 1.2 1 239314 24375 58 144120 1.2 1 130493 13627 59 189763 1.2 1 174150 15613 60 221672 1.2 1 202663 19009 61 204715 1.2 1 187874 16841 62 167001 1.2 1 153283 13718 63 255251 1.2 1 234100 21151 64 130506 1.2 1 118894 11612 65 139928 1.2 1 129142 10786 66 105154 1.2 1 96331 8823 67 154060 1.2 1 141982 12078 68 150876 1.2 1 138995 11881 69 139705 1.2 1 128831 10874 70 148155 1.2 1 136963 11192 71 145133 1.2 1 134141 10992 72 143299 1.2 1 132435 10864 73 174094 1.2 1 161212 12882 74 140058 1.2 1 129978 10080 75 128886 1.2 1 120401 8485 76 82374 1.2 1 76690 5684 77 77132 1.2 1 71228 5904 78 82100 1.2 1 76270 5830 79 81894 1.2 1 75912 5982 80 83573 1.2 1 77583 5990 81 83132 1.2 1 77284 5848 82 79030 1.2 1 73599 5431 83 73898 1.2 1 68964 4934 84 68613 1.2 1 63878 4735 85 66146 1.2 1 61618 4528 86 61283 1.2 1 57196 4087 87 57917 1.2 1 54163 3754 88 54983 1.2 1 51435 3548 89 54394 1.2 1 50831 3563 90 54067 1.2 1 50772 3295 91 51240 1.2 1 48050 3190 92 49026 1.2 1 45974 3052 93 45712 1.2 1 42912 2800 94 41227 1.2 1 38776 2451 95 37736 1.2 1 35499 2237 96 35021 1.2 1 32961 2060 97 32314 1.2 1 30368 1946 98 30314 1.2 1 28467 1847 99 29454 1.2 1 27742 1712 100 28091 1.2 1 26556 1535 101 25246 1.2 1 23769 1477 102 23890 1.2 1 22569 1321 103 21256 1.2 1 20124 1132 104 18451 1.2 1 17438 1013 105 16716 1.2 1 15836 880 106 14879 1.2 1 14068 811 107 13379 1.2 1 12684 695 108 12053 1.2 1 11452 601 109 10512 1.2 1 9976 536 110 9292 1.2 1 8850 442 111 8119 1.2 1 7719 400 112 7586 1.2 1 7205 381 113 6467 1.2 1 6143 324 114 5325 1.2 1 5065 260 115 4394 1.2 1 4208 186 116 3674 1.2 1 3519 155 117 2944 1.2 1 2805 139 118 2420 1.2 1 2323 97 119 1953 1.2 1 1840 113 120 1996 1.2 1 1893 103 121 1268 1.2 1 1188 80 122 996 1.2 1 938 58 123 716 1.2 1 668 48 124 510 1.2 1 476 34 125 371 1.2 1 335 36 126 326 1.2 1 305 21 127 183 1.2 1 167 16 128 138 1.2 1 126 12 129 130 1.2 1 114 16 130 121 1.2 1 109 12 131 104 1.2 1 96 8 132 59 1.2 1 51 8 133 93 1.2 1 87 6 134 47 1.2 1 38 9 135 52 1.2 1 47 5 136 37 1.2 1 30 7 137 63 1.2 1 53 10 138 29 1.2 1 21 8 139 59 1.2 1 47 12 140 40 1.2 1 30 10 141 52 1.2 1 42 10 142 32 1.2 1 16 16 143 37 1.2 1 25 12 144 29 1.2 1 14 15 145 48 1.2 1 25 23 146 33 1.2 1 15 18 147 31 1.2 1 21 10 148 37 1.2 1 15 22 149 42 1.2 1 27 15 150 25 1.2 1 10 15 151 117 1.2 1 81 36 RUN STATISTICS FOR INPUT FILE: ERR10683998_1.fastq.gz ============================================= 78491837 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 78491837 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25377 (0.03%)