SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245586_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: 86040). 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 SRR18245586_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4080.818 s (49.338 µs/read; 1.22 M reads/minute). === Summary === Total reads processed: 82,712,035 Reads with adapters: 46,314,544 (56.0%) Reads written (passing filters): 82,712,035 (100.0%) Total basepairs processed: 12,406,805,250 bp Quality-trimmed: 34,668,782 bp (0.3%) Total written (filtered): 12,034,913,313 bp (97.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46314544 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.7% C: 20.0% G: 0.4% T: 31.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 35964338 20678008.8 0 35964338 2 390487 5169502.2 0 390487 3 378167 1292375.5 0 378167 4 343321 323093.9 0 343321 5 336869 80773.5 0 336869 6 278302 20193.4 0 278302 7 283781 5048.3 0 283781 8 306176 1262.1 0 306176 9 233512 315.5 0 232480 1032 10 276221 78.9 1 254638 21583 11 267814 19.7 1 241815 25999 12 268434 4.9 1 243987 24447 13 242712 1.2 1 222550 20162 14 249172 1.2 1 226054 23118 15 224047 1.2 1 205391 18656 16 231793 1.2 1 210278 21515 17 239124 1.2 1 219681 19443 18 183204 1.2 1 168486 14718 19 218033 1.2 1 199827 18206 20 210062 1.2 1 193366 16696 21 174047 1.2 1 157416 16631 22 180936 1.2 1 167175 13761 23 171995 1.2 1 160074 11921 24 191746 1.2 1 176721 15025 25 192186 1.2 1 179040 13146 26 126401 1.2 1 115560 10841 27 141286 1.2 1 128988 12298 28 147245 1.2 1 137864 9381 29 138443 1.2 1 127186 11257 30 138495 1.2 1 128416 10079 31 124841 1.2 1 116017 8824 32 123871 1.2 1 115609 8262 33 134072 1.2 1 124607 9465 34 109828 1.2 1 100228 9600 35 109024 1.2 1 101265 7759 36 109957 1.2 1 103531 6426 37 98302 1.2 1 91504 6798 38 95951 1.2 1 89550 6401 39 99797 1.2 1 93073 6724 40 84204 1.2 1 78783 5421 41 86017 1.2 1 80870 5147 42 112646 1.2 1 106611 6035 43 57333 1.2 1 52455 4878 44 135031 1.2 1 128694 6337 45 89449 1.2 1 83798 5651 46 58927 1.2 1 52730 6197 47 138751 1.2 1 134644 4107 48 21251 1.2 1 18636 2615 49 61356 1.2 1 57457 3899 50 23735 1.2 1 21983 1752 51 38134 1.2 1 35318 2816 52 26229 1.2 1 24116 2113 53 51428 1.2 1 48893 2535 54 80434 1.2 1 77382 3052 55 21094 1.2 1 19052 2042 56 51333 1.2 1 47426 3907 57 174662 1.2 1 170130 4532 58 28925 1.2 1 26645 2280 59 15113 1.2 1 13163 1950 60 96800 1.2 1 93829 2971 61 16162 1.2 1 14899 1263 62 13800 1.2 1 12060 1740 63 78925 1.2 1 75665 3260 64 103772 1.2 1 101364 2408 65 10792 1.2 1 9702 1090 66 21385 1.2 1 20089 1296 67 12952 1.2 1 12291 661 68 9106 1.2 1 8204 902 69 13382 1.2 1 12537 845 70 20542 1.2 1 19598 944 71 8474 1.2 1 7877 597 72 7885 1.2 1 7263 622 73 9879 1.2 1 9137 742 74 10743 1.2 1 9967 776 75 16150 1.2 1 15081 1069 76 20173 1.2 1 19008 1165 77 18383 1.2 1 17407 976 78 19485 1.2 1 18602 883 79 19723 1.2 1 18828 895 80 19742 1.2 1 18857 885 81 19338 1.2 1 18477 861 82 19390 1.2 1 18474 916 83 21386 1.2 1 20462 924 84 19984 1.2 1 19039 945 85 21237 1.2 1 20274 963 86 18569 1.2 1 17681 888 87 17033 1.2 1 16260 773 88 16151 1.2 1 15373 778 89 15486 1.2 1 14794 692 90 15241 1.2 1 14576 665 91 14724 1.2 1 14121 603 92 14434 1.2 1 13826 608 93 13834 1.2 1 13268 566 94 13625 1.2 1 13020 605 95 13226 1.2 1 12630 596 96 12671 1.2 1 12090 581 97 12831 1.2 1 12265 566 98 12739 1.2 1 12219 520 99 12964 1.2 1 12417 547 100 12567 1.2 1 12061 506 101 11610 1.2 1 11136 474 102 11019 1.2 1 10543 476 103 10665 1.2 1 10195 470 104 10077 1.2 1 9612 465 105 10006 1.2 1 9557 449 106 9998 1.2 1 9576 422 107 9703 1.2 1 9292 411 108 9592 1.2 1 9194 398 109 9376 1.2 1 8945 431 110 9388 1.2 1 9019 369 111 9385 1.2 1 8992 393 112 9143 1.2 1 8768 375 113 9306 1.2 1 8936 370 114 8567 1.2 1 8185 382 115 7983 1.2 1 7638 345 116 8107 1.2 1 7745 362 117 7806 1.2 1 7452 354 118 7628 1.2 1 7222 406 119 7659 1.2 1 7255 404 120 7610 1.2 1 7195 415 121 7341 1.2 1 6898 443 122 7278 1.2 1 6744 534 123 7918 1.2 1 7167 751 124 7412 1.2 1 6603 809 125 7352 1.2 1 6370 982 126 7096 1.2 1 5894 1202 127 6815 1.2 1 5465 1350 128 6681 1.2 1 5198 1483 129 6707 1.2 1 5032 1675 130 6257 1.2 1 4425 1832 131 6525 1.2 1 4323 2202 132 6242 1.2 1 3793 2449 133 6253 1.2 1 3574 2679 134 5736 1.2 1 3066 2670 135 5279 1.2 1 2743 2536 136 4648 1.2 1 2265 2383 137 3780 1.2 1 2104 1676 138 3294 1.2 1 2146 1148 139 2765 1.2 1 1931 834 140 2553 1.2 1 1924 629 141 2738 1.2 1 2205 533 142 2190 1.2 1 1786 404 143 2197 1.2 1 1788 409 144 2924 1.2 1 2373 551 145 3359 1.2 1 2738 621 146 1836 1.2 1 1437 399 147 311 1.2 1 206 105 148 3778 1.2 1 3123 655 149 1612 1.2 1 1277 335 150 35310 1.2 1 30225 5085 RUN STATISTICS FOR INPUT FILE: SRR18245586_2.fastq.gz ============================================= 82712035 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82712035 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 129009 (0.16%)