SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684004_2.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: 282233). 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 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR10684004_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1968.400 s (16.785 µs/read; 3.57 M reads/minute). === Summary === Total reads processed: 117,273,904 Reads with adapters: 81,545,838 (69.5%) Reads written (passing filters): 117,273,904 (100.0%) Total basepairs processed: 17,708,359,504 bp Quality-trimmed: 61,493,706 bp (0.3%) Total written (filtered): 16,180,056,587 bp (91.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 81545838 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.7% C: 19.0% G: 0.7% T: 28.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 36172298 29318476.0 0 36172298 2 1250091 7329619.0 0 1250091 3 1077168 1832404.8 0 1077168 4 874328 458101.2 0 874328 5 948830 114525.3 0 948830 6 933220 28631.3 0 933220 7 939592 7157.8 0 939592 8 1119327 1789.5 0 1119327 9 778404 447.4 0 775961 2443 10 983263 111.8 1 905706 77557 11 867718 28.0 1 808165 59553 12 914756 7.0 1 801870 112886 13 872008 1.7 1 763215 108793 14 1022929 1.7 1 887797 135132 15 695571 1.7 1 614413 81158 16 871401 1.7 1 772649 98752 17 1071493 1.7 1 944592 126901 18 685742 1.7 1 608175 77567 19 1036415 1.7 1 911683 124732 20 892810 1.7 1 792181 100629 21 620080 1.7 1 553240 66840 22 770052 1.7 1 683939 86113 23 756355 1.7 1 670030 86325 24 867975 1.7 1 757203 110772 25 828128 1.7 1 735952 92176 26 652394 1.7 1 580646 71748 27 648507 1.7 1 574298 74209 28 839644 1.7 1 747782 91862 29 715618 1.7 1 640414 75204 30 827941 1.7 1 738995 88946 31 669076 1.7 1 598831 70245 32 683153 1.7 1 606176 76977 33 641255 1.7 1 571931 69324 34 611911 1.7 1 547008 64903 35 555789 1.7 1 500625 55164 36 636845 1.7 1 573712 63133 37 594334 1.7 1 533832 60502 38 653159 1.7 1 594499 58660 39 443030 1.7 1 399238 43792 40 604306 1.7 1 546019 58287 41 567767 1.7 1 512991 54776 42 579703 1.7 1 523783 55920 43 421034 1.7 1 381650 39384 44 456300 1.7 1 411797 44503 45 465484 1.7 1 420393 45091 46 441957 1.7 1 401490 40467 47 437787 1.7 1 396151 41636 48 430050 1.7 1 391442 38608 49 462793 1.7 1 420716 42077 50 438335 1.7 1 400358 37977 51 402336 1.7 1 367457 34879 52 390565 1.7 1 357467 33098 53 364526 1.7 1 332176 32350 54 402765 1.7 1 367097 35668 55 269552 1.7 1 246466 23086 56 331501 1.7 1 302614 28887 57 436963 1.7 1 399783 37180 58 237067 1.7 1 215565 21502 59 317593 1.7 1 293093 24500 60 375406 1.7 1 344383 31023 61 345475 1.7 1 318547 26928 62 271649 1.7 1 250084 21565 63 413592 1.7 1 382090 31502 64 208371 1.7 1 190908 17463 65 215908 1.7 1 199850 16058 66 161920 1.7 1 149003 12917 67 240202 1.7 1 222299 17903 68 235823 1.7 1 218100 17723 69 218986 1.7 1 202588 16398 70 234185 1.7 1 216919 17266 71 229220 1.7 1 212582 16638 72 221841 1.7 1 205538 16303 73 257314 1.7 1 239339 17975 74 200494 1.7 1 186800 13694 75 175304 1.7 1 163703 11601 76 107082 1.7 1 99643 7439 77 108114 1.7 1 100370 7744 78 115952 1.7 1 108146 7806 79 118055 1.7 1 110068 7987 80 120410 1.7 1 112291 8119 81 120641 1.7 1 112577 8064 82 110142 1.7 1 103028 7114 83 99314 1.7 1 92886 6428 84 90942 1.7 1 85146 5796 85 83617 1.7 1 78151 5466 86 78191 1.7 1 73241 4950 87 73119 1.7 1 68502 4617 88 68799 1.7 1 64598 4201 89 67853 1.7 1 63680 4173 90 67505 1.7 1 63378 4127 91 63399 1.7 1 59593 3806 92 59077 1.7 1 55560 3517 93 53485 1.7 1 50443 3042 94 45808 1.7 1 43215 2593 95 41485 1.7 1 39150 2335 96 37418 1.7 1 35240 2178 97 34192 1.7 1 32294 1898 98 32128 1.7 1 30389 1739 99 30799 1.7 1 29115 1684 100 28931 1.7 1 27491 1440 101 25983 1.7 1 24610 1373 102 23584 1.7 1 22388 1196 103 20873 1.7 1 19805 1068 104 18344 1.7 1 17431 913 105 15984 1.7 1 15197 787 106 14177 1.7 1 13464 713 107 12486 1.7 1 11882 604 108 10824 1.7 1 10298 526 109 9583 1.7 1 9132 451 110 8208 1.7 1 7830 378 111 7583 1.7 1 7226 357 112 6446 1.7 1 6154 292 113 5752 1.7 1 5526 226 114 4382 1.7 1 4208 174 115 3602 1.7 1 3420 182 116 3032 1.7 1 2895 137 117 2347 1.7 1 2264 83 118 1848 1.7 1 1750 98 119 1528 1.7 1 1454 74 120 1686 1.7 1 1607 79 121 1036 1.7 1 982 54 122 739 1.7 1 702 37 123 507 1.7 1 477 30 124 399 1.7 1 378 21 125 319 1.7 1 296 23 126 208 1.7 1 190 18 127 159 1.7 1 148 11 128 104 1.7 1 88 16 129 97 1.7 1 83 14 130 77 1.7 1 62 15 131 74 1.7 1 60 14 132 42 1.7 1 31 11 133 56 1.7 1 45 11 134 50 1.7 1 40 10 135 37 1.7 1 32 5 136 39 1.7 1 25 14 137 44 1.7 1 31 13 138 25 1.7 1 14 11 139 27 1.7 1 16 11 140 32 1.7 1 10 22 141 34 1.7 1 18 16 142 18 1.7 1 7 11 143 28 1.7 1 9 19 144 23 1.7 1 9 14 145 28 1.7 1 15 13 146 27 1.7 1 3 24 147 35 1.7 1 14 21 148 32 1.7 1 7 25 149 36 1.7 1 22 14 150 27 1.7 1 11 16 151 85 1.7 1 57 28 RUN STATISTICS FOR INPUT FILE: ERR10684004_2.fastq.gz ============================================= 117273904 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 117273904 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 26667 (0.02%)