SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684002_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: 260252). 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 ERR10684002_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1712.844 s (16.551 µs/read; 3.63 M reads/minute). === Summary === Total reads processed: 103,490,578 Reads with adapters: 71,612,413 (69.2%) Reads written (passing filters): 103,490,578 (100.0%) Total basepairs processed: 15,627,077,278 bp Quality-trimmed: 56,781,745 bp (0.4%) Total written (filtered): 14,406,504,272 bp (92.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 71612413 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.1% C: 19.2% G: 0.7% T: 28.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33119157 25872644.5 0 33119157 2 1116850 6468161.1 0 1116850 3 1044570 1617040.3 0 1044570 4 876821 404260.1 0 876821 5 933778 101065.0 0 933778 6 917682 25266.3 0 917682 7 919660 6316.6 0 919660 8 1085325 1579.1 0 1085325 9 765467 394.8 0 762436 3031 10 924668 98.7 1 850554 74114 11 823930 24.7 1 763528 60402 12 845593 6.2 1 726169 119424 13 798586 1.5 1 684127 114459 14 950851 1.5 1 809334 141517 15 607918 1.5 1 524744 83174 16 793781 1.5 1 687483 106298 17 991060 1.5 1 855692 135368 18 619663 1.5 1 536118 83545 19 918578 1.5 1 791727 126851 20 778548 1.5 1 675060 103488 21 580257 1.5 1 505641 74616 22 663907 1.5 1 577734 86173 23 643457 1.5 1 557955 85502 24 712664 1.5 1 609848 102816 25 706643 1.5 1 614723 91920 26 556357 1.5 1 484789 71568 27 555257 1.5 1 481513 73744 28 697663 1.5 1 608395 89268 29 640724 1.5 1 560693 80031 30 685834 1.5 1 600632 85202 31 583356 1.5 1 511295 72061 32 545609 1.5 1 474818 70791 33 516395 1.5 1 450963 65432 34 524514 1.5 1 462369 62145 35 407478 1.5 1 356713 50765 36 451582 1.5 1 397514 54068 37 464094 1.5 1 408526 55568 38 598726 1.5 1 530208 68518 39 500113 1.5 1 442438 57675 40 368852 1.5 1 326298 42554 41 435459 1.5 1 388160 47299 42 441610 1.5 1 393385 48225 43 323402 1.5 1 287444 35958 44 350736 1.5 1 310867 39869 45 352613 1.5 1 313098 39515 46 338270 1.5 1 301343 36927 47 328812 1.5 1 292169 36643 48 339660 1.5 1 303028 36632 49 363562 1.5 1 324832 38730 50 338522 1.5 1 303384 35138 51 309853 1.5 1 277401 32452 52 297283 1.5 1 267280 30003 53 275345 1.5 1 246403 28942 54 297611 1.5 1 267095 30516 55 202895 1.5 1 181860 21035 56 245665 1.5 1 220177 25488 57 333682 1.5 1 301318 32364 58 173094 1.5 1 154555 18539 59 242006 1.5 1 219059 22947 60 287872 1.5 1 259802 28070 61 262498 1.5 1 237647 24851 62 206525 1.5 1 186718 19807 63 303263 1.5 1 275887 27376 64 148164 1.5 1 133113 15051 65 158940 1.5 1 144579 14361 66 119196 1.5 1 107832 11364 67 172545 1.5 1 157151 15394 68 172511 1.5 1 157014 15497 69 161290 1.5 1 146902 14388 70 172970 1.5 1 157901 15069 71 171455 1.5 1 156559 14896 72 163054 1.5 1 148888 14166 73 187080 1.5 1 171319 15761 74 146715 1.5 1 134378 12337 75 127027 1.5 1 116992 10035 76 78064 1.5 1 71648 6416 77 78260 1.5 1 71704 6556 78 82451 1.5 1 75770 6681 79 82423 1.5 1 75740 6683 80 85088 1.5 1 78306 6782 81 85061 1.5 1 78178 6883 82 77958 1.5 1 71808 6150 83 70777 1.5 1 65300 5477 84 63237 1.5 1 58261 4976 85 60047 1.5 1 55439 4608 86 54844 1.5 1 50763 4081 87 50799 1.5 1 47067 3732 88 48222 1.5 1 44621 3601 89 46531 1.5 1 43160 3371 90 46269 1.5 1 42915 3354 91 43016 1.5 1 39961 3055 92 40418 1.5 1 37588 2830 93 36674 1.5 1 34137 2537 94 31060 1.5 1 29001 2059 95 28230 1.5 1 26257 1973 96 25656 1.5 1 23873 1783 97 22900 1.5 1 21381 1519 98 21328 1.5 1 19896 1432 99 20521 1.5 1 19168 1353 100 19335 1.5 1 18044 1291 101 16941 1.5 1 15822 1119 102 15227 1.5 1 14285 942 103 13359 1.5 1 12565 794 104 11453 1.5 1 10704 749 105 10143 1.5 1 9564 579 106 8842 1.5 1 8340 502 107 8030 1.5 1 7561 469 108 6889 1.5 1 6474 415 109 5857 1.5 1 5504 353 110 5077 1.5 1 4784 293 111 4585 1.5 1 4323 262 112 3752 1.5 1 3535 217 113 3263 1.5 1 3094 169 114 2402 1.5 1 2277 125 115 1956 1.5 1 1842 114 116 1660 1.5 1 1566 94 117 1238 1.5 1 1180 58 118 1020 1.5 1 955 65 119 829 1.5 1 781 48 120 899 1.5 1 850 49 121 537 1.5 1 488 49 122 356 1.5 1 333 23 123 295 1.5 1 268 27 124 192 1.5 1 168 24 125 152 1.5 1 129 23 126 109 1.5 1 104 5 127 91 1.5 1 80 11 128 81 1.5 1 77 4 129 87 1.5 1 72 15 130 74 1.5 1 53 21 131 72 1.5 1 58 14 132 58 1.5 1 46 12 133 47 1.5 1 42 5 134 34 1.5 1 30 4 135 43 1.5 1 31 12 136 32 1.5 1 25 7 137 35 1.5 1 30 5 138 37 1.5 1 22 15 139 32 1.5 1 19 13 140 24 1.5 1 16 8 141 23 1.5 1 14 9 142 17 1.5 1 3 14 143 24 1.5 1 14 10 144 17 1.5 1 4 13 145 38 1.5 1 13 25 146 23 1.5 1 9 14 147 22 1.5 1 5 17 148 24 1.5 1 6 18 149 31 1.5 1 18 13 150 19 1.5 1 10 9 151 43 1.5 1 29 14 RUN STATISTICS FOR INPUT FILE: ERR10684002_2.fastq.gz ============================================= 103490578 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 103490578 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17209 (0.02%)