SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308528_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: 123417). 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 ERR12308528_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1109.482 s (16.985 µs/read; 3.53 M reads/minute). === Summary === Total reads processed: 65,320,260 Reads with adapters: 36,014,531 (55.1%) Reads written (passing filters): 65,320,260 (100.0%) Total basepairs processed: 9,863,359,260 bp Quality-trimmed: 56,176,833 bp (0.6%) Total written (filtered): 9,452,835,547 bp (95.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36014531 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.2% C: 19.5% G: 2.9% T: 28.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24192906 16330065.0 0 24192906 2 750841 4082516.2 0 750841 3 405899 1020629.1 0 405899 4 275543 255157.3 0 275543 5 290373 63789.3 0 290373 6 257033 15947.3 0 257033 7 250484 3986.8 0 250484 8 306563 996.7 0 306563 9 161003 249.2 0 160491 512 10 264261 62.3 1 233267 30994 11 226668 15.6 1 202468 24200 12 249075 3.9 1 210812 38263 13 237193 1.0 1 200441 36752 14 273866 1.0 1 227280 46586 15 200833 1.0 1 170833 30000 16 226659 1.0 1 192205 34454 17 246797 1.0 1 210657 36140 18 191286 1.0 1 163287 27999 19 244656 1.0 1 205114 39542 20 250059 1.0 1 213272 36787 21 155456 1.0 1 132982 22474 22 206889 1.0 1 175937 30952 23 205559 1.0 1 174781 30778 24 241815 1.0 1 203234 38581 25 238112 1.0 1 204143 33969 26 154622 1.0 1 130976 23646 27 160053 1.0 1 136288 23765 28 205705 1.0 1 177592 28113 29 156704 1.0 1 135754 20950 30 198759 1.0 1 170606 28153 31 152865 1.0 1 131521 21344 32 196829 1.0 1 168518 28311 33 167540 1.0 1 144717 22823 34 147874 1.0 1 128120 19754 35 179217 1.0 1 154892 24325 36 137708 1.0 1 121541 16167 37 153743 1.0 1 133894 19849 38 147524 1.0 1 129881 17643 39 130547 1.0 1 114453 16094 40 135575 1.0 1 118807 16768 41 133628 1.0 1 117411 16217 42 148445 1.0 1 130219 18226 43 108781 1.0 1 95209 13572 44 126048 1.0 1 109773 16275 45 131394 1.0 1 114741 16653 46 110958 1.0 1 97457 13501 47 115415 1.0 1 102016 13399 48 100862 1.0 1 89017 11845 49 104639 1.0 1 92186 12453 50 98218 1.0 1 87583 10635 51 93307 1.0 1 82710 10597 52 93800 1.0 1 83211 10589 53 88267 1.0 1 78709 9558 54 101094 1.0 1 90448 10646 55 66242 1.0 1 59339 6903 56 82034 1.0 1 73105 8929 57 106519 1.0 1 94801 11718 58 53544 1.0 1 47689 5855 59 59664 1.0 1 53985 5679 60 76133 1.0 1 68453 7680 61 67692 1.0 1 61142 6550 62 49162 1.0 1 44246 4916 63 106875 1.0 1 96832 10043 64 47123 1.0 1 42439 4684 65 35063 1.0 1 31707 3356 66 33653 1.0 1 30370 3283 67 55308 1.0 1 50550 4758 68 47319 1.0 1 43080 4239 69 39178 1.0 1 35696 3482 70 43044 1.0 1 39472 3572 71 38561 1.0 1 35353 3208 72 37329 1.0 1 34178 3151 73 47203 1.0 1 43422 3781 74 32085 1.0 1 29390 2695 75 30834 1.0 1 28368 2466 76 18435 1.0 1 16946 1489 77 18561 1.0 1 17021 1540 78 19412 1.0 1 17818 1594 79 18785 1.0 1 17322 1463 80 18275 1.0 1 16861 1414 81 17554 1.0 1 16127 1427 82 16267 1.0 1 14984 1283 83 15807 1.0 1 14580 1227 84 14692 1.0 1 13600 1092 85 14095 1.0 1 13057 1038 86 12570 1.0 1 11581 989 87 11613 1.0 1 10796 817 88 10579 1.0 1 9880 699 89 10123 1.0 1 9393 730 90 9528 1.0 1 8839 689 91 8575 1.0 1 7968 607 92 8293 1.0 1 7729 564 93 7708 1.0 1 7144 564 94 6885 1.0 1 6392 493 95 6386 1.0 1 5907 479 96 6010 1.0 1 5572 438 97 5425 1.0 1 5049 376 98 5193 1.0 1 4828 365 99 4925 1.0 1 4545 380 100 4564 1.0 1 4212 352 101 3871 1.0 1 3553 318 102 3380 1.0 1 3116 264 103 3134 1.0 1 2904 230 104 2801 1.0 1 2571 230 105 2643 1.0 1 2451 192 106 2474 1.0 1 2289 185 107 2241 1.0 1 2066 175 108 1926 1.0 1 1766 160 109 1828 1.0 1 1694 134 110 1541 1.0 1 1440 101 111 1378 1.0 1 1269 109 112 1262 1.0 1 1145 117 113 1204 1.0 1 1105 99 114 964 1.0 1 864 100 115 878 1.0 1 798 80 116 771 1.0 1 688 83 117 746 1.0 1 659 87 118 617 1.0 1 549 68 119 628 1.0 1 566 62 120 891 1.0 1 825 66 121 610 1.0 1 551 59 122 412 1.0 1 356 56 123 367 1.0 1 305 62 124 306 1.0 1 261 45 125 269 1.0 1 222 47 126 282 1.0 1 234 48 127 220 1.0 1 181 39 128 210 1.0 1 169 41 129 182 1.0 1 146 36 130 142 1.0 1 110 32 131 146 1.0 1 127 19 132 107 1.0 1 90 17 133 116 1.0 1 99 17 134 73 1.0 1 54 19 135 112 1.0 1 87 25 136 80 1.0 1 67 13 137 88 1.0 1 76 12 138 76 1.0 1 60 16 139 74 1.0 1 60 14 140 62 1.0 1 49 13 141 57 1.0 1 38 19 142 37 1.0 1 25 12 143 40 1.0 1 30 10 144 36 1.0 1 25 11 145 34 1.0 1 24 10 146 41 1.0 1 25 16 147 53 1.0 1 29 24 148 49 1.0 1 29 20 149 43 1.0 1 29 14 150 31 1.0 1 21 10 151 223 1.0 1 67 156 RUN STATISTICS FOR INPUT FILE: ERR12308528_2.fastq.gz ============================================= 65320260 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 65320260 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 41695 (0.06%)