SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308525_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: 78406). 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 ERR12308525_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1634.120 s (18.939 µs/read; 3.17 M reads/minute). === Summary === Total reads processed: 86,285,288 Reads with adapters: 46,251,653 (53.6%) Reads written (passing filters): 86,285,288 (100.0%) Total basepairs processed: 13,029,078,488 bp Quality-trimmed: 72,376,293 bp (0.6%) Total written (filtered): 12,644,317,106 bp (97.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46251653 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.6% C: 19.6% G: 1.3% T: 28.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 36037119 21571322.0 0 36037119 2 554800 5392830.5 0 554800 3 379762 1348207.6 0 379762 4 272137 337051.9 0 272137 5 288538 84263.0 0 288538 6 255163 21065.7 0 255163 7 238808 5266.4 0 238808 8 288597 1316.6 0 288597 9 168070 329.2 0 167676 394 10 246139 82.3 1 220391 25748 11 221433 20.6 1 199176 22257 12 230495 5.1 1 189879 40616 13 230253 1.3 1 186154 44099 14 250698 1.3 1 201514 49184 15 186262 1.3 1 153724 32538 16 222001 1.3 1 181331 40670 17 209285 1.3 1 172544 36741 18 190954 1.3 1 157466 33488 19 222815 1.3 1 181423 41392 20 222788 1.3 1 183863 38925 21 129086 1.3 1 106492 22594 22 180350 1.3 1 148057 32293 23 177878 1.3 1 145783 32095 24 210412 1.3 1 171373 39039 25 212327 1.3 1 175436 36891 26 131925 1.3 1 108019 23906 27 129998 1.3 1 107066 22932 28 168467 1.3 1 140823 27644 29 139907 1.3 1 117047 22860 30 153119 1.3 1 126958 26161 31 137728 1.3 1 114423 23305 32 140357 1.3 1 116607 23750 33 135197 1.3 1 112368 22829 34 138762 1.3 1 116725 22037 35 120873 1.3 1 102105 18768 36 129518 1.3 1 108473 21045 37 136069 1.3 1 114308 21761 38 118550 1.3 1 100024 18526 39 110892 1.3 1 94586 16306 40 98217 1.3 1 82686 15531 41 105816 1.3 1 89827 15989 42 109825 1.3 1 93777 16048 43 87718 1.3 1 74554 13164 44 96831 1.3 1 82135 14696 45 101169 1.3 1 85660 15509 46 88065 1.3 1 74530 13535 47 87189 1.3 1 74896 12293 48 81750 1.3 1 69725 12025 49 81696 1.3 1 69805 11891 50 76835 1.3 1 66288 10547 51 72401 1.3 1 62388 10013 52 73270 1.3 1 62795 10475 53 68818 1.3 1 59525 9293 54 76303 1.3 1 66002 10301 55 53982 1.3 1 46691 7291 56 63803 1.3 1 55167 8636 57 80261 1.3 1 69686 10575 58 42588 1.3 1 36778 5810 59 49064 1.3 1 42985 6079 60 57600 1.3 1 50442 7158 61 53568 1.3 1 46841 6727 62 40988 1.3 1 35951 5037 63 78481 1.3 1 69360 9121 64 38236 1.3 1 33458 4778 65 29940 1.3 1 26317 3623 66 28290 1.3 1 24856 3434 67 43122 1.3 1 38390 4732 68 38292 1.3 1 33879 4413 69 32051 1.3 1 28524 3527 70 34338 1.3 1 30589 3749 71 31571 1.3 1 28236 3335 72 31481 1.3 1 28037 3444 73 40536 1.3 1 36339 4197 74 28884 1.3 1 25885 2999 75 27722 1.3 1 25039 2683 76 15469 1.3 1 13832 1637 77 15776 1.3 1 14210 1566 78 16787 1.3 1 15104 1683 79 16138 1.3 1 14608 1530 80 15580 1.3 1 14067 1513 81 15053 1.3 1 13656 1397 82 14461 1.3 1 13159 1302 83 14023 1.3 1 12710 1313 84 13195 1.3 1 11959 1236 85 12940 1.3 1 11731 1209 86 11880 1.3 1 10843 1037 87 10747 1.3 1 9834 913 88 9969 1.3 1 9113 856 89 9594 1.3 1 8772 822 90 9275 1.3 1 8475 800 91 8255 1.3 1 7566 689 92 8027 1.3 1 7411 616 93 7501 1.3 1 6895 606 94 6562 1.3 1 6037 525 95 6271 1.3 1 5735 536 96 5920 1.3 1 5463 457 97 5399 1.3 1 4975 424 98 5229 1.3 1 4848 381 99 5009 1.3 1 4638 371 100 4853 1.3 1 4482 371 101 4015 1.3 1 3696 319 102 3627 1.3 1 3348 279 103 3199 1.3 1 2992 207 104 3013 1.3 1 2804 209 105 2722 1.3 1 2544 178 106 2421 1.3 1 2234 187 107 2252 1.3 1 2076 176 108 2114 1.3 1 1983 131 109 1881 1.3 1 1732 149 110 1829 1.3 1 1691 138 111 1486 1.3 1 1376 110 112 1286 1.3 1 1197 89 113 1127 1.3 1 1053 74 114 1069 1.3 1 982 87 115 898 1.3 1 828 70 116 751 1.3 1 684 67 117 719 1.3 1 663 56 118 630 1.3 1 565 65 119 523 1.3 1 476 47 120 528 1.3 1 472 56 121 485 1.3 1 452 33 122 379 1.3 1 342 37 123 274 1.3 1 229 45 124 261 1.3 1 216 45 125 226 1.3 1 198 28 126 187 1.3 1 157 30 127 152 1.3 1 129 23 128 132 1.3 1 109 23 129 90 1.3 1 76 14 130 88 1.3 1 70 18 131 79 1.3 1 65 14 132 72 1.3 1 61 11 133 79 1.3 1 67 12 134 61 1.3 1 52 9 135 67 1.3 1 46 21 136 50 1.3 1 44 6 137 65 1.3 1 53 12 138 54 1.3 1 40 14 139 50 1.3 1 33 17 140 38 1.3 1 30 8 141 65 1.3 1 47 18 142 38 1.3 1 20 18 143 32 1.3 1 16 16 144 39 1.3 1 17 22 145 46 1.3 1 33 13 146 33 1.3 1 18 15 147 49 1.3 1 27 22 148 32 1.3 1 15 17 149 39 1.3 1 23 16 150 13 1.3 1 5 8 151 142 1.3 1 43 99 RUN STATISTICS FOR INPUT FILE: ERR12308525_2.fastq.gz ============================================= 86285288 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 86285288 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 43364 (0.05%)