SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245590_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: 268362). 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 SRR18245590_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3973.830 s (42.143 µs/read; 1.42 M reads/minute). === Summary === Total reads processed: 94,292,827 Reads with adapters: 61,399,485 (65.1%) Reads written (passing filters): 94,292,827 (100.0%) Total basepairs processed: 14,143,924,050 bp Quality-trimmed: 68,943,950 bp (0.5%) Total written (filtered): 11,990,565,214 bp (84.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 61399485 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.0% C: 17.2% G: 1.4% T: 33.8% none/other: 3.7% Overview of removed sequences length count expect max.err error counts 1 32073728 23573206.8 0 32073728 2 432252 5893301.7 0 432252 3 427885 1473325.4 0 427885 4 393984 368331.4 0 393984 5 388901 92082.8 0 388901 6 324549 23020.7 0 324549 7 334424 5755.2 0 334424 8 365429 1438.8 0 365429 9 286000 359.7 0 284645 1355 10 339865 89.9 1 313009 26856 11 337723 22.5 1 301127 36596 12 341019 5.6 1 308554 32465 13 314275 1.4 1 286627 27648 14 326216 1.4 1 295306 30910 15 295955 1.4 1 269508 26447 16 311764 1.4 1 281281 30483 17 329878 1.4 1 302137 27741 18 253953 1.4 1 232111 21842 19 307920 1.4 1 280881 27039 20 304980 1.4 1 279260 25720 21 254170 1.4 1 228310 25860 22 267891 1.4 1 246901 20990 23 259452 1.4 1 239887 19565 24 298888 1.4 1 273728 25160 25 297856 1.4 1 276207 21649 26 206595 1.4 1 188034 18561 27 229190 1.4 1 206858 22332 28 244398 1.4 1 227708 16690 29 234610 1.4 1 212712 21898 30 236528 1.4 1 218844 17684 31 219449 1.4 1 202339 17110 32 219386 1.4 1 204169 15217 33 247314 1.4 1 228707 18607 34 208794 1.4 1 187182 21612 35 206661 1.4 1 190518 16143 36 214143 1.4 1 200489 13654 37 196130 1.4 1 181136 14994 38 191986 1.4 1 177587 14399 39 207149 1.4 1 191935 15214 40 175756 1.4 1 162642 13114 41 185437 1.4 1 173358 12079 42 260038 1.4 1 245311 14727 43 129355 1.4 1 116264 13091 44 338464 1.4 1 322084 16380 45 240830 1.4 1 224995 15835 46 145436 1.4 1 127463 17973 47 330877 1.4 1 319712 11165 48 61016 1.4 1 52332 8684 49 173737 1.4 1 161178 12559 50 55275 1.4 1 50125 5150 51 105496 1.4 1 96610 8886 52 64719 1.4 1 58311 6408 53 142648 1.4 1 134766 7882 54 232761 1.4 1 223663 9098 55 66631 1.4 1 59436 7195 56 159010 1.4 1 144631 14379 57 619934 1.4 1 603920 16014 58 100034 1.4 1 90816 9218 59 52106 1.4 1 44675 7431 60 349419 1.4 1 338459 10960 61 60969 1.4 1 56375 4594 62 47188 1.4 1 40636 6552 63 302963 1.4 1 289317 13646 64 431337 1.4 1 421682 9655 65 45470 1.4 1 40745 4725 66 90582 1.4 1 85348 5234 67 51500 1.4 1 48760 2740 68 38966 1.4 1 34844 4122 69 58780 1.4 1 54947 3833 70 97134 1.4 1 92747 4387 71 42509 1.4 1 39365 3144 72 40338 1.4 1 37051 3287 73 56215 1.4 1 52000 4215 74 71285 1.4 1 65165 6120 75 123227 1.4 1 113108 10119 76 157580 1.4 1 147100 10480 77 108337 1.4 1 100389 7948 78 111948 1.4 1 105714 6234 79 113511 1.4 1 107358 6153 80 117238 1.4 1 111220 6018 81 120358 1.4 1 114048 6310 82 128286 1.4 1 120520 7766 83 157486 1.4 1 149240 8246 84 148572 1.4 1 139643 8929 85 168586 1.4 1 160029 8557 86 144256 1.4 1 136542 7714 87 130638 1.4 1 122788 7850 88 127918 1.4 1 120206 7712 89 121524 1.4 1 115631 5893 90 122850 1.4 1 117720 5130 91 119017 1.4 1 114274 4743 92 121671 1.4 1 116832 4839 93 121781 1.4 1 117014 4767 94 122007 1.4 1 116988 5019 95 122065 1.4 1 117088 4977 96 124211 1.4 1 119237 4974 97 126617 1.4 1 121606 5011 98 133907 1.4 1 128923 4984 99 139914 1.4 1 135140 4774 100 143426 1.4 1 138606 4820 101 133541 1.4 1 128788 4753 102 129670 1.4 1 124977 4693 103 128310 1.4 1 123734 4576 104 127525 1.4 1 122974 4551 105 132000 1.4 1 127474 4526 106 133196 1.4 1 128589 4607 107 135092 1.4 1 130451 4641 108 137160 1.4 1 132493 4667 109 134947 1.4 1 130243 4704 110 137190 1.4 1 132324 4866 111 143825 1.4 1 138931 4894 112 148924 1.4 1 144034 4890 113 150299 1.4 1 145245 5054 114 154685 1.4 1 149767 4918 115 147826 1.4 1 142905 4921 116 147407 1.4 1 142146 5261 117 147204 1.4 1 141885 5319 118 152558 1.4 1 147160 5398 119 156069 1.4 1 150280 5789 120 160138 1.4 1 153941 6197 121 161688 1.4 1 155280 6408 122 161988 1.4 1 155119 6869 123 180228 1.4 1 171915 8313 124 170535 1.4 1 162460 8075 125 174879 1.4 1 165509 9370 126 168873 1.4 1 158034 10839 127 160794 1.4 1 147761 13033 128 165270 1.4 1 148047 17223 129 178043 1.4 1 151671 26372 130 174125 1.4 1 135011 39114 131 193630 1.4 1 132950 60680 132 210964 1.4 1 126513 84451 133 225140 1.4 1 121508 103632 134 216530 1.4 1 110049 106481 135 209396 1.4 1 101383 108013 136 189475 1.4 1 88259 101216 137 163072 1.4 1 87329 75743 138 145560 1.4 1 92386 53174 139 129146 1.4 1 90178 38968 140 123401 1.4 1 92866 30535 141 139077 1.4 1 116948 22129 142 110482 1.4 1 95873 14609 143 120396 1.4 1 105317 15079 144 150977 1.4 1 130657 20320 145 183515 1.4 1 156326 27189 146 99729 1.4 1 80578 19151 147 20286 1.4 1 14390 5896 148 234583 1.4 1 199113 35470 149 93093 1.4 1 75623 17470 150 2174608 1.4 1 1916651 257957 RUN STATISTICS FOR INPUT FILE: SRR18245590_2.fastq.gz ============================================= 94292827 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 94292827 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5781588 (6.13%)