SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684006_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: 304222). Second best hit was smallRNA (count: 1) 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 ERR10684006_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1621.630 s (19.279 µs/read; 3.11 M reads/minute). === Summary === Total reads processed: 84,111,724 Reads with adapters: 59,955,017 (71.3%) Reads written (passing filters): 84,111,724 (100.0%) Total basepairs processed: 12,700,870,324 bp Quality-trimmed: 43,734,600 bp (0.3%) Total written (filtered): 11,536,491,975 bp (90.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 59955017 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.8% C: 19.2% G: 0.7% T: 28.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24522147 21027931.0 0 24522147 2 937768 5256982.8 0 937768 3 853790 1314245.7 0 853790 4 687892 328561.4 0 687892 5 748765 82140.4 0 748765 6 738135 20535.1 0 738135 7 739590 5133.8 0 739590 8 875226 1283.4 0 875226 9 613839 320.9 0 611968 1871 10 767422 80.2 1 699974 67448 11 688355 20.1 1 635011 53344 12 719114 5.0 1 618548 100566 13 691254 1.3 1 591490 99764 14 833550 1.3 1 708459 125091 15 537808 1.3 1 464937 72871 16 683479 1.3 1 592920 90559 17 916191 1.3 1 793060 123131 18 474166 1.3 1 409897 64269 19 854764 1.3 1 737898 116866 20 683549 1.3 1 593960 89589 21 475377 1.3 1 414679 60698 22 615482 1.3 1 535149 80333 23 606586 1.3 1 527356 79230 24 711683 1.3 1 609652 102031 25 700954 1.3 1 611099 89855 26 516185 1.3 1 451226 64959 27 469438 1.3 1 407102 62336 28 684796 1.3 1 599464 85332 29 540742 1.3 1 474351 66391 30 664040 1.3 1 582136 81904 31 515975 1.3 1 453370 62605 32 549415 1.3 1 479875 69540 33 470415 1.3 1 413657 56758 34 496889 1.3 1 434071 62818 35 483937 1.3 1 426301 57636 36 545234 1.3 1 481753 63481 37 394800 1.3 1 346720 48080 38 489222 1.3 1 433223 55999 39 555002 1.3 1 493779 61223 40 366266 1.3 1 325258 41008 41 436701 1.3 1 389331 47370 42 446057 1.3 1 397606 48451 43 341058 1.3 1 303942 37116 44 366388 1.3 1 326075 40313 45 371290 1.3 1 330093 41197 46 352779 1.3 1 314469 38310 47 344914 1.3 1 307131 37783 48 348568 1.3 1 311531 37037 49 362754 1.3 1 324524 38230 50 342915 1.3 1 307783 35132 51 317776 1.3 1 285429 32347 52 306318 1.3 1 275537 30781 53 290120 1.3 1 260596 29524 54 318113 1.3 1 285670 32443 55 217226 1.3 1 195351 21875 56 261884 1.3 1 235128 26756 57 342384 1.3 1 308834 33550 58 183489 1.3 1 164301 19188 59 245994 1.3 1 223082 22912 60 282305 1.3 1 255487 26818 61 259520 1.3 1 235568 23952 62 212962 1.3 1 193124 19838 63 311091 1.3 1 283272 27819 64 157554 1.3 1 142195 15359 65 171299 1.3 1 156117 15182 66 125402 1.3 1 113810 11592 67 179867 1.3 1 163951 15916 68 176474 1.3 1 160694 15780 69 160015 1.3 1 146295 13720 70 168212 1.3 1 153737 14475 71 164844 1.3 1 150412 14432 72 159337 1.3 1 145602 13735 73 181806 1.3 1 166589 15217 74 147942 1.3 1 135755 12187 75 127988 1.3 1 117942 10046 76 78854 1.3 1 72388 6466 77 78283 1.3 1 71687 6596 78 81202 1.3 1 74642 6560 79 79571 1.3 1 73119 6452 80 80460 1.3 1 74038 6422 81 79371 1.3 1 73059 6312 82 72526 1.3 1 66849 5677 83 65472 1.3 1 60479 4993 84 60009 1.3 1 55520 4489 85 56141 1.3 1 51841 4300 86 51789 1.3 1 47910 3879 87 48260 1.3 1 44637 3623 88 44676 1.3 1 41331 3345 89 43423 1.3 1 40186 3237 90 42554 1.3 1 39536 3018 91 39208 1.3 1 36426 2782 92 36527 1.3 1 33900 2627 93 33186 1.3 1 30832 2354 94 29172 1.3 1 27105 2067 95 26540 1.3 1 24719 1821 96 24352 1.3 1 22775 1577 97 21770 1.3 1 20354 1416 98 20687 1.3 1 19264 1423 99 19560 1.3 1 18340 1220 100 18023 1.3 1 16898 1125 101 15864 1.3 1 14905 959 102 14149 1.3 1 13257 892 103 12344 1.3 1 11621 723 104 10955 1.3 1 10327 628 105 9715 1.3 1 9132 583 106 8314 1.3 1 7834 480 107 7464 1.3 1 7020 444 108 6709 1.3 1 6296 413 109 5811 1.3 1 5496 315 110 4991 1.3 1 4725 266 111 4286 1.3 1 4035 251 112 3823 1.3 1 3608 215 113 3108 1.3 1 2943 165 114 2543 1.3 1 2397 146 115 2012 1.3 1 1910 102 116 1558 1.3 1 1472 86 117 1396 1.3 1 1336 60 118 1089 1.3 1 1037 52 119 878 1.3 1 832 46 120 919 1.3 1 880 39 121 536 1.3 1 493 43 122 415 1.3 1 400 15 123 307 1.3 1 276 31 124 240 1.3 1 225 15 125 186 1.3 1 165 21 126 131 1.3 1 123 8 127 97 1.3 1 85 12 128 98 1.3 1 89 9 129 73 1.3 1 63 10 130 68 1.3 1 55 13 131 71 1.3 1 58 13 132 52 1.3 1 44 8 133 51 1.3 1 45 6 134 41 1.3 1 27 14 135 57 1.3 1 43 14 136 37 1.3 1 30 7 137 41 1.3 1 29 12 138 24 1.3 1 19 5 139 18 1.3 1 14 4 140 27 1.3 1 19 8 141 32 1.3 1 25 7 142 17 1.3 1 10 7 143 28 1.3 1 15 13 144 20 1.3 1 4 16 145 44 1.3 1 25 19 146 24 1.3 1 11 13 147 26 1.3 1 11 15 148 20 1.3 1 10 10 149 30 1.3 1 18 12 150 17 1.3 1 6 11 151 57 1.3 1 31 26 RUN STATISTICS FOR INPUT FILE: ERR10684006_1.fastq.gz ============================================= 84111724 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84111724 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19681 (0.02%)