SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684000_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: 232627). 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 ERR10684000_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1407.545 s (18.645 µs/read; 3.22 M reads/minute). === Summary === Total reads processed: 75,491,417 Reads with adapters: 50,483,803 (66.9%) Reads written (passing filters): 75,491,417 (100.0%) Total basepairs processed: 11,399,203,967 bp Quality-trimmed: 44,779,741 bp (0.4%) Total written (filtered): 10,562,886,769 bp (92.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 50483803 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.3% C: 19.0% G: 1.0% T: 27.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24718566 18872854.2 0 24718566 2 1065248 4718213.6 0 1065248 3 699157 1179553.4 0 699157 4 592595 294888.3 0 592595 5 617288 73722.1 0 617288 6 607587 18430.5 0 607587 7 612957 4607.6 0 612957 8 729819 1151.9 0 729819 9 483860 288.0 0 482432 1428 10 616417 72.0 1 550299 66118 11 533397 18.0 1 482146 51251 12 557641 4.5 1 485979 71662 13 516253 1.1 1 450444 65809 14 628425 1.1 1 543402 85023 15 387219 1.1 1 340682 46537 16 503897 1.1 1 446099 57798 17 680232 1.1 1 599134 81098 18 362973 1.1 1 320466 42507 19 608198 1.1 1 532899 75299 20 510372 1.1 1 451741 58631 21 353339 1.1 1 314854 38485 22 425066 1.1 1 376750 48316 23 411039 1.1 1 363944 47095 24 432867 1.1 1 377642 55225 25 467945 1.1 1 414644 53301 26 363459 1.1 1 322712 40747 27 355824 1.1 1 313952 41872 28 440939 1.1 1 392469 48470 29 409272 1.1 1 365858 43414 30 452640 1.1 1 403762 48878 31 361569 1.1 1 323893 37676 32 354338 1.1 1 314009 40329 33 332009 1.1 1 295889 36120 34 345321 1.1 1 309642 35679 35 274838 1.1 1 244882 29956 36 306076 1.1 1 274974 31102 37 357920 1.1 1 323911 34009 38 299927 1.1 1 271437 28490 39 224804 1.1 1 203138 21666 40 313168 1.1 1 283150 30018 41 294179 1.1 1 265734 28445 42 294130 1.1 1 265153 28977 43 215307 1.1 1 195235 20072 44 229267 1.1 1 206893 22374 45 233720 1.1 1 210914 22806 46 224481 1.1 1 203596 20885 47 216489 1.1 1 195812 20677 48 217996 1.1 1 198434 19562 49 237585 1.1 1 216062 21523 50 219233 1.1 1 200387 18846 51 203215 1.1 1 185741 17474 52 195658 1.1 1 178966 16692 53 183163 1.1 1 166758 16405 54 199504 1.1 1 181840 17664 55 134274 1.1 1 122972 11302 56 164958 1.1 1 150306 14652 57 222301 1.1 1 202812 19489 58 116340 1.1 1 105710 10630 59 158474 1.1 1 146195 12279 60 188143 1.1 1 172716 15427 61 173728 1.1 1 160328 13400 62 138400 1.1 1 127465 10935 63 207316 1.1 1 191147 16169 64 102281 1.1 1 93713 8568 65 109684 1.1 1 101581 8103 66 81582 1.1 1 75166 6416 67 118783 1.1 1 109877 8906 68 118512 1.1 1 109490 9022 69 108792 1.1 1 100587 8205 70 116368 1.1 1 107661 8707 71 115195 1.1 1 106757 8438 72 111768 1.1 1 103635 8133 73 132672 1.1 1 123355 9317 74 105836 1.1 1 98338 7498 75 92182 1.1 1 86024 6158 76 58759 1.1 1 54770 3989 77 57659 1.1 1 53452 4207 78 60714 1.1 1 56367 4347 79 60792 1.1 1 56591 4201 80 62374 1.1 1 58005 4369 81 62733 1.1 1 58465 4268 82 58508 1.1 1 54445 4063 83 54052 1.1 1 50477 3575 84 49830 1.1 1 46368 3462 85 46906 1.1 1 43823 3083 86 44375 1.1 1 41511 2864 87 40809 1.1 1 38159 2650 88 39225 1.1 1 36689 2536 89 38228 1.1 1 35782 2446 90 38397 1.1 1 35986 2411 91 35877 1.1 1 33574 2303 92 34520 1.1 1 32286 2234 93 31988 1.1 1 30022 1966 94 28407 1.1 1 26665 1742 95 25821 1.1 1 24234 1587 96 23721 1.1 1 22251 1470 97 21876 1.1 1 20585 1291 98 20892 1.1 1 19667 1225 99 20272 1.1 1 19023 1249 100 19217 1.1 1 18138 1079 101 17288 1.1 1 16306 982 102 15806 1.1 1 14884 922 103 14119 1.1 1 13293 826 104 12678 1.1 1 11943 735 105 11348 1.1 1 10729 619 106 10071 1.1 1 9522 549 107 9329 1.1 1 8850 479 108 8240 1.1 1 7799 441 109 7572 1.1 1 7171 401 110 6862 1.1 1 6500 362 111 6124 1.1 1 5828 296 112 5334 1.1 1 5048 286 113 4699 1.1 1 4461 238 114 3873 1.1 1 3709 164 115 3283 1.1 1 3100 183 116 2621 1.1 1 2487 134 117 2257 1.1 1 2149 108 118 1869 1.1 1 1788 81 119 1504 1.1 1 1425 79 120 1965 1.1 1 1885 80 121 1041 1.1 1 979 62 122 839 1.1 1 800 39 123 614 1.1 1 583 31 124 433 1.1 1 412 21 125 330 1.1 1 294 36 126 253 1.1 1 232 21 127 177 1.1 1 158 19 128 135 1.1 1 119 16 129 124 1.1 1 111 13 130 109 1.1 1 90 19 131 116 1.1 1 94 22 132 60 1.1 1 48 12 133 94 1.1 1 83 11 134 44 1.1 1 40 4 135 59 1.1 1 50 9 136 40 1.1 1 29 11 137 44 1.1 1 28 16 138 27 1.1 1 17 10 139 35 1.1 1 26 9 140 31 1.1 1 22 9 141 47 1.1 1 38 9 142 22 1.1 1 13 9 143 25 1.1 1 18 7 144 23 1.1 1 7 16 145 42 1.1 1 11 31 146 30 1.1 1 3 27 147 42 1.1 1 18 24 148 31 1.1 1 10 21 149 46 1.1 1 27 19 150 21 1.1 1 6 15 151 98 1.1 1 74 24 RUN STATISTICS FOR INPUT FILE: ERR10684000_1.fastq.gz ============================================= 75491417 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 75491417 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33365 (0.04%)