SUMMARISING RUN PARAMETERS ========================== Input filename: juvenile_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.7 Cutadapt version: 3.4 Python version: could not detect Number of cores used for trimming: 4 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 1702). Second best hit was Nextera (count: 7) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 2-colour high quality G-trimming enabled, with quality cutoff: --nextseq-trim=20 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 Output file will be GZIP compressed This is cutadapt 3.4 with Python 3.9.6 Command line parameters: -j 4 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC juvenile_2.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 3506.80 s (11 µs/read; 5.63 M reads/minute). === Summary === Total reads processed: 328,998,671 Reads with adapters: 89,303,228 (27.1%) Reads written (passing filters): 328,998,671 (100.0%) Total basepairs processed: 47,481,512,510 bp Quality-trimmed: 943,009,163 bp (2.0%) Total written (filtered): 46,260,170,896 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 89303228 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.4% C: 24.4% G: 13.8% T: 20.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 80057849 82249667.8 0 80057849 3 4941630 5140604.2 0 4941630 4 1456947 1285151.1 0 1456947 5 349161 321287.8 0 349161 8 21326 5020.1 0 21326 9 24540 1255.0 0 24540 10 2563 313.8 1 0 2563 11 43195 78.4 1 18105 25090 12 9412 19.6 1 0 9412 13 109033 4.9 1 49606 59427 14 14571 4.9 1 1471 13100 15 17733 4.9 1 5836 11897 16 56924 4.9 1 18330 38594 17 19278 4.9 1 5567 13711 18 10320 4.9 1 3823 6497 19 18870 4.9 1 8272 10598 20 17629 4.9 1 8096 9533 21 27106 4.9 1 14246 12860 22 20422 4.9 1 11464 8958 23 1545 4.9 1 1047 498 24 6218 4.9 1 3759 2459 25 22846 4.9 1 12959 9887 26 33473 4.9 1 17990 15483 27 37691 4.9 1 22304 15387 28 16947 4.9 1 11797 5150 29 14492 4.9 1 7857 6635 30 20494 4.9 1 14778 5716 31 7820 4.9 1 5483 2337 32 50301 4.9 1 37646 12655 33 8213 4.9 1 3674 4539 34 41504 4.9 1 28607 12897 35 1345 4.9 1 872 473 36 3874 4.9 1 2136 1738 37 6229 4.9 1 4564 1665 38 10204 4.9 1 6627 3577 39 28236 4.9 1 20886 7350 40 14989 4.9 1 7833 7156 41 23103 4.9 1 16112 6991 42 13201 4.9 1 10136 3065 43 2407 4.9 1 1041 1366 44 13969 4.9 1 9846 4123 45 3420 4.9 1 2627 793 46 10021 4.9 1 7265 2756 47 5440 4.9 1 3190 2250 48 13456 4.9 1 9610 3846 49 13090 4.9 1 9450 3640 50 7836 4.9 1 4445 3391 51 13366 4.9 1 9417 3949 52 1859 4.9 1 1046 813 53 4984 4.9 1 3487 1497 54 6744 4.9 1 4797 1947 55 4694 4.9 1 2628 2066 56 8928 4.9 1 5933 2995 57 6231 4.9 1 4219 2012 58 6400 4.9 1 3992 2408 59 7757 4.9 1 4995 2762 60 5171 4.9 1 3311 1860 61 5447 4.9 1 3230 2217 62 5002 4.9 1 3051 1951 63 4771 4.9 1 2863 1908 64 4548 4.9 1 2667 1881 65 4418 4.9 1 2559 1859 66 5521 4.9 1 2779 2742 67 46668 4.9 1 3845 42823 68 125381 4.9 1 4355 121026 69 117027 4.9 1 4128 112899 70 142260 4.9 1 3645 138615 71 109314 4.9 1 2313 107001 72 83559 4.9 1 1450 82109 73 57580 4.9 1 978 56602 74 41205 4.9 1 764 40441 75 39820 4.9 1 678 39142 76 28472 4.9 1 591 27881 77 23224 4.9 1 575 22649 78 26137 4.9 1 473 25664 79 24885 4.9 1 485 24400 80 26897 4.9 1 427 26470 81 26651 4.9 1 399 26252 82 22995 4.9 1 403 22592 83 18728 4.9 1 334 18394 84 17015 4.9 1 287 16728 85 14049 4.9 1 279 13770 86 10778 4.9 1 253 10525 87 9652 4.9 1 270 9382 88 8340 4.9 1 271 8069 89 6867 4.9 1 214 6653 90 6202 4.9 1 241 5961 91 5621 4.9 1 229 5392 92 4427 4.9 1 233 4194 93 4005 4.9 1 213 3792 94 3612 4.9 1 175 3437 95 3309 4.9 1 197 3112 96 3149 4.9 1 190 2959 97 2821 4.9 1 162 2659 98 2586 4.9 1 193 2393 99 2437 4.9 1 190 2247 100 2453 4.9 1 210 2243 101 2254 4.9 1 188 2066 102 2152 4.9 1 207 1945 103 2403 4.9 1 200 2203 104 2265 4.9 1 156 2109 105 2585 4.9 1 196 2389 106 2616 4.9 1 169 2447 107 3001 4.9 1 195 2806 108 2674 4.9 1 144 2530 109 3169 4.9 1 168 3001 110 3272 4.9 1 175 3097 111 3677 4.9 1 154 3523 112 3406 4.9 1 157 3249 113 3571 4.9 1 179 3392 114 3844 4.9 1 164 3680 115 3196 4.9 1 173 3023 116 2801 4.9 1 128 2673 117 2637 4.9 1 136 2501 118 2512 4.9 1 118 2394 119 2260 4.9 1 75 2185 120 2114 4.9 1 121 1993 121 2000 4.9 1 111 1889 122 1711 4.9 1 94 1617 123 1579 4.9 1 99 1480 124 1552 4.9 1 92 1460 125 1485 4.9 1 97 1388 126 1790 4.9 1 103 1687 127 1202 4.9 1 69 1133 128 1124 4.9 1 53 1071 129 1260 4.9 1 78 1182 130 1187 4.9 1 53 1134 131 897 4.9 1 60 837 132 933 4.9 1 55 878 133 888 4.9 1 54 834 134 919 4.9 1 47 872 135 993 4.9 1 43 950 136 930 4.9 1 22 908 137 957 4.9 1 35 922 138 1244 4.9 1 43 1201 139 1247 4.9 1 28 1219 140 1285 4.9 1 12 1273 141 1636 4.9 1 22 1614 142 1841 4.9 1 12 1829 143 2422 4.9 1 7 2415 144 3137 4.9 1 3 3134 145 4311 4.9 1 14 4297 146 6402 4.9 1 8 6394 147 11016 4.9 1 15 11001 148 21909 4.9 1 11 21898 149 42027 4.9 1 4 42023 150 247813 4.9 1 1 247812 151 64282 4.9 1 0 64282 RUN STATISTICS FOR INPUT FILE: juvenile_2.fastq.gz ============================================= 328998671 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 328998671 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2313848 (0.70%)