SUMMARISING RUN PARAMETERS ========================== Input filename: HB_trimmed_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.9 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 2731). Second best hit was smallRNA (count: 17) 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: -t 12 Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.8 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HB_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 322.720 s (4.062 µs/read; 14.77 M reads/minute). === Summary === Total reads processed: 79,451,611 Reads with adapters: 21,825,839 (27.5%) Reads written (passing filters): 79,451,611 (100.0%) Total basepairs processed: 11,141,672,714 bp Quality-trimmed: 196,791,925 bp (1.8%) Total written (filtered): 10,584,505,166 bp (95.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21825839 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.8% C: 33.8% G: 31.6% T: 10.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 8084406 19862902.8 0 8084406 2 4102544 4965725.7 0 4102544 3 729988 1241431.4 0 729988 4 83019 310357.9 0 83019 5 27780 77589.5 0 27780 6 7495 19397.4 0 7495 7 4747 4849.3 0 4747 8 2592 1212.3 0 2592 9 12780 303.1 0 9484 3296 10 8322 75.8 1 4593 3729 11 12467 18.9 1 6450 6017 12 18589 4.7 1 10907 7682 13 7890 1.2 1 3407 4483 14 13901 1.2 1 6770 7131 15 20491 1.2 1 10844 9647 16 17971 1.2 1 9302 8669 17 30537 1.2 1 19598 10939 18 37591 1.2 1 22362 15229 19 162218 1.2 1 127374 34844 20 59373 1.2 1 45789 13584 21 19270 1.2 1 11393 7877 22 25058 1.2 1 14395 10663 23 45084 1.2 1 26761 18323 24 575174 1.2 1 516730 58444 25 203086 1.2 1 171871 31215 26 216141 1.2 1 187838 28303 27 1564339 1.2 1 1503903 60436 28 176626 1.2 1 158046 18580 29 533572 1.2 1 511646 21926 30 119616 1.2 1 111099 8517 31 59002 1.2 1 51397 7605 32 326616 1.2 1 308546 18070 33 130459 1.2 1 112167 18292 34 937502 1.2 1 903999 33503 35 204412 1.2 1 186757 17655 36 545296 1.2 1 521699 23597 37 58794 1.2 1 51368 7426 38 110953 1.2 1 105180 5773 39 34908 1.2 1 30519 4389 40 115864 1.2 1 104475 11389 41 283793 1.2 1 268957 14836 42 46445 1.2 1 40236 6209 43 49832 1.2 1 44595 5237 44 44688 1.2 1 36563 8125 45 143895 1.2 1 134228 9667 46 45059 1.2 1 40634 4425 47 34871 1.2 1 30785 4086 48 7555 1.2 1 6049 1506 49 32240 1.2 1 28953 3287 50 96739 1.2 1 91249 5490 51 26810 1.2 1 22636 4174 52 59456 1.2 1 55613 3843 53 52602 1.2 1 48467 4135 54 25500 1.2 1 22001 3499 55 79068 1.2 1 75041 4027 56 27539 1.2 1 24474 3065 57 35367 1.2 1 32413 2954 58 37941 1.2 1 34812 3129 59 84034 1.2 1 78479 5555 60 46904 1.2 1 43051 3853 61 35531 1.2 1 31567 3964 62 73331 1.2 1 69504 3827 63 24931 1.2 1 21612 3319 64 50928 1.2 1 47754 3174 65 28855 1.2 1 26216 2639 66 31444 1.2 1 28533 2911 67 39361 1.2 1 36280 3081 68 65442 1.2 1 61740 3702 69 53194 1.2 1 49741 3453 70 33024 1.2 1 30172 2852 71 62728 1.2 1 59798 2930 72 34768 1.2 1 32006 2762 73 36582 1.2 1 34299 2283 74 45583 1.2 1 43362 2221 75 46223 1.2 1 44337 1886 76 19286 1.2 1 18193 1093 77 4869 1.2 1 4202 667 78 6590 1.2 1 5886 704 79 12548 1.2 1 11680 868 80 16104 1.2 1 15155 949 81 18157 1.2 1 17107 1050 82 17956 1.2 1 16777 1179 83 17554 1.2 1 16455 1099 84 16802 1.2 1 15745 1057 85 15172 1.2 1 14194 978 86 13755 1.2 1 12862 893 87 12778 1.2 1 12056 722 88 12061 1.2 1 11269 792 89 11469 1.2 1 10780 689 90 10761 1.2 1 10094 667 91 10076 1.2 1 9455 621 92 9350 1.2 1 8764 586 93 8745 1.2 1 8246 499 94 7930 1.2 1 7470 460 95 7176 1.2 1 6845 331 96 6442 1.2 1 6120 322 97 6041 1.2 1 5750 291 98 5341 1.2 1 5067 274 99 5160 1.2 1 4868 292 100 4666 1.2 1 4450 216 101 4267 1.2 1 4062 205 102 3974 1.2 1 3728 246 103 3381 1.2 1 3200 181 104 3094 1.2 1 2894 200 105 2865 1.2 1 2676 189 106 2425 1.2 1 2298 127 107 2382 1.2 1 2234 148 108 2149 1.2 1 2008 141 109 2013 1.2 1 1842 171 110 1804 1.2 1 1666 138 111 1601 1.2 1 1493 108 112 1497 1.2 1 1375 122 113 1375 1.2 1 1248 127 114 1372 1.2 1 1264 108 115 1256 1.2 1 1137 119 116 1301 1.2 1 1181 120 117 1133 1.2 1 1018 115 118 1202 1.2 1 1043 159 119 1112 1.2 1 1013 99 120 1024 1.2 1 920 104 121 992 1.2 1 877 115 122 1076 1.2 1 964 112 123 1089 1.2 1 968 121 124 1103 1.2 1 1019 84 125 1207 1.2 1 1109 98 126 1273 1.2 1 1155 118 127 1488 1.2 1 1354 134 128 1642 1.2 1 1508 134 129 1780 1.2 1 1609 171 130 2071 1.2 1 1902 169 131 2152 1.2 1 1980 172 132 2554 1.2 1 2347 207 133 2943 1.2 1 2715 228 134 4463 1.2 1 4201 262 135 3775 1.2 1 3581 194 136 4008 1.2 1 3780 228 137 4917 1.2 1 4635 282 138 5445 1.2 1 5143 302 139 5061 1.2 1 4744 317 140 6012 1.2 1 5589 423 141 9087 1.2 1 8519 568 142 4941 1.2 1 4619 322 143 5908 1.2 1 5577 331 144 7456 1.2 1 7038 418 145 9009 1.2 1 8580 429 146 15370 1.2 1 14639 731 147 18832 1.2 1 17822 1010 148 5835 1.2 1 5442 393 149 1048 1.2 1 500 548 150 6550 1.2 1 4911 1639 RUN STATISTICS FOR INPUT FILE: HB_trimmed_2.fastq.gz ============================================= 79451611 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 79451611 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2663907 (3.35%)