SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245591_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 51919). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245591_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4198.874 s (51.125 µs/read; 1.17 M reads/minute). === Summary === Total reads processed: 82,128,972 Reads with adapters: 43,922,945 (53.5%) Reads written (passing filters): 82,128,972 (100.0%) Total basepairs processed: 12,319,345,800 bp Quality-trimmed: 44,163,101 bp (0.4%) Total written (filtered): 12,027,914,580 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43922945 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.3% C: 18.1% G: 0.3% T: 31.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 38125194 20532243.0 0 38125194 2 173003 5133060.8 0 173003 3 171839 1283265.2 0 171839 4 149899 320816.3 0 149899 5 147889 80204.1 0 147889 6 123511 20051.0 0 123511 7 126303 5012.8 0 126303 8 138850 1253.2 0 138850 9 100817 313.3 0 100374 443 10 123589 78.3 1 113810 9779 11 116912 19.6 1 105350 11562 12 118877 4.9 1 107380 11497 13 111938 1.2 1 101744 10194 14 115908 1.2 1 104947 10961 15 102091 1.2 1 93230 8861 16 106171 1.2 1 96900 9271 17 119459 1.2 1 109879 9580 18 80459 1.2 1 73316 7143 19 122674 1.2 1 112757 9917 20 86773 1.2 1 79500 7273 21 76671 1.2 1 69494 7177 22 87013 1.2 1 80176 6837 23 85050 1.2 1 78792 6258 24 107151 1.2 1 98676 8475 25 95770 1.2 1 89155 6615 26 63101 1.2 1 57968 5133 27 61819 1.2 1 56328 5491 28 79611 1.2 1 74513 5098 29 67484 1.2 1 62302 5182 30 75485 1.2 1 70669 4816 31 63924 1.2 1 59503 4421 32 68525 1.2 1 64114 4411 33 69953 1.2 1 65081 4872 34 81375 1.2 1 75640 5735 35 62938 1.2 1 58631 4307 36 51108 1.2 1 46523 4585 37 86271 1.2 1 82370 3901 38 44029 1.2 1 40923 3106 39 58284 1.2 1 54277 4007 40 75086 1.2 1 70132 4954 41 28498 1.2 1 24910 3588 42 60854 1.2 1 57845 3009 43 52111 1.2 1 46573 5538 44 188525 1.2 1 181707 6818 45 58945 1.2 1 55105 3840 46 19137 1.2 1 16867 2270 47 58985 1.2 1 57036 1949 48 18557 1.2 1 17152 1405 49 26317 1.2 1 24343 1974 50 16172 1.2 1 15299 873 51 20963 1.2 1 19561 1402 52 12491 1.2 1 11569 922 53 32900 1.2 1 31453 1447 54 49488 1.2 1 47763 1725 55 22893 1.2 1 21486 1407 56 35496 1.2 1 33659 1837 57 62932 1.2 1 60937 1995 58 28132 1.2 1 26636 1496 59 25173 1.2 1 23838 1335 60 51133 1.2 1 49392 1741 61 34122 1.2 1 32923 1199 62 18000 1.2 1 16869 1131 63 54324 1.2 1 52147 2177 64 87852 1.2 1 85836 2016 65 37517 1.2 1 36200 1317 66 35175 1.2 1 33886 1289 67 37552 1.2 1 36680 872 68 12523 1.2 1 11789 734 69 18300 1.2 1 17591 709 70 24001 1.2 1 23332 669 71 11107 1.2 1 10649 458 72 6926 1.2 1 6573 353 73 6613 1.2 1 6275 338 74 7222 1.2 1 6862 360 75 8797 1.2 1 8333 464 76 12572 1.2 1 11982 590 77 13209 1.2 1 12523 686 78 16880 1.2 1 16195 685 79 18844 1.2 1 18099 745 80 19973 1.2 1 19215 758 81 20138 1.2 1 19321 817 82 20181 1.2 1 19353 828 83 21767 1.2 1 20950 817 84 21087 1.2 1 20227 860 85 22191 1.2 1 21298 893 86 20037 1.2 1 19236 801 87 18432 1.2 1 17715 717 88 18162 1.2 1 17390 772 89 17283 1.2 1 16566 717 90 17148 1.2 1 16481 667 91 16542 1.2 1 15896 646 92 16169 1.2 1 15523 646 93 15842 1.2 1 15194 648 94 15149 1.2 1 14525 624 95 14940 1.2 1 14326 614 96 14708 1.2 1 14141 567 97 14284 1.2 1 13704 580 98 14418 1.2 1 13816 602 99 14684 1.2 1 14118 566 100 14366 1.2 1 13811 555 101 13432 1.2 1 12875 557 102 12475 1.2 1 11966 509 103 12134 1.2 1 11652 482 104 11551 1.2 1 11052 499 105 11398 1.2 1 10957 441 106 10895 1.2 1 10389 506 107 10855 1.2 1 10339 516 108 10462 1.2 1 10010 452 109 9927 1.2 1 9534 393 110 9665 1.2 1 9254 411 111 9397 1.2 1 9003 394 112 9200 1.2 1 8811 389 113 8734 1.2 1 8330 404 114 8577 1.2 1 8205 372 115 8388 1.2 1 8013 375 116 8461 1.2 1 8068 393 117 7935 1.2 1 7554 381 118 7917 1.2 1 7513 404 119 7360 1.2 1 6963 397 120 7102 1.2 1 6624 478 121 6889 1.2 1 6353 536 122 6668 1.2 1 5983 685 123 6433 1.2 1 5604 829 124 6320 1.2 1 5220 1100 125 6246 1.2 1 4949 1297 126 5951 1.2 1 4454 1497 127 5793 1.2 1 4079 1714 128 5691 1.2 1 3841 1850 129 5134 1.2 1 3234 1900 130 4611 1.2 1 2912 1699 131 4255 1.2 1 2749 1506 132 3646 1.2 1 2407 1239 133 3464 1.2 1 2201 1263 134 3212 1.2 1 1961 1251 135 2719 1.2 1 1624 1095 136 2430 1.2 1 1380 1050 137 1973 1.2 1 1186 787 138 1751 1.2 1 1168 583 139 1431 1.2 1 987 444 140 1367 1.2 1 1001 366 141 1450 1.2 1 1171 279 142 1186 1.2 1 979 207 143 1070 1.2 1 869 201 144 1561 1.2 1 1257 304 145 1934 1.2 1 1547 387 146 949 1.2 1 677 272 147 127 1.2 1 64 63 148 941 1.2 1 697 244 149 374 1.2 1 266 108 150 9961 1.2 1 8266 1695 RUN STATISTICS FOR INPUT FILE: SRR18245591_2.fastq.gz ============================================= 82128972 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82128972 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 60383 (0.07%)