SUMMARISING RUN PARAMETERS ========================== Input filename: juvenile_1.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_1.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 3676.53 s (11 µs/read; 5.37 M reads/minute). === Summary === Total reads processed: 328,998,671 Reads with adapters: 79,783,864 (24.3%) Reads written (passing filters): 328,998,671 (100.0%) Total basepairs processed: 47,511,600,333 bp Quality-trimmed: 876,883,681 bp (1.8%) Total written (filtered): 46,370,976,242 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 79783864 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.2% C: 29.1% G: 12.1% T: 20.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 72207806 82249667.8 0 72207806 3 3610337 5140604.2 0 3610337 4 1154452 1285151.1 0 1154452 5 262345 321287.8 0 262345 8 15332 5020.1 0 15332 9 11626 1255.0 0 11626 10 3027 313.8 1 0 3027 11 17690 78.4 1 6009 11681 12 11001 19.6 1 0 11001 13 16062 4.9 1 3007 13055 14 32138 4.9 1 3833 28305 15 21696 4.9 1 3466 18230 16 41644 4.9 1 10638 31006 17 35498 4.9 1 7348 28150 18 27674 4.9 1 11577 16097 19 16659 4.9 1 5494 11165 20 38616 4.9 1 13375 25241 21 22244 4.9 1 9352 12892 22 36279 4.9 1 19602 16677 23 7241 4.9 1 3059 4182 24 27020 4.9 1 13242 13778 25 20458 4.9 1 8131 12327 26 29697 4.9 1 16679 13018 27 44694 4.9 1 21174 23520 28 32100 4.9 1 13929 18171 29 37491 4.9 1 24152 13339 30 14807 4.9 1 9143 5664 31 23559 4.9 1 12830 10729 32 17837 4.9 1 11515 6322 33 46977 4.9 1 30331 16646 34 12276 4.9 1 6305 5971 35 48451 4.9 1 31141 17310 36 12793 4.9 1 6783 6010 37 32395 4.9 1 22770 9625 38 23941 4.9 1 14420 9521 39 15976 4.9 1 10126 5850 40 29953 4.9 1 19289 10664 41 12580 4.9 1 8248 4332 42 19754 4.9 1 12609 7145 43 10203 4.9 1 6720 3483 44 16453 4.9 1 10838 5615 45 8267 4.9 1 5408 2859 46 19120 4.9 1 12014 7106 47 6127 4.9 1 4046 2081 48 21889 4.9 1 14475 7414 49 3520 4.9 1 2308 1212 50 18087 4.9 1 11875 6212 51 6103 4.9 1 3543 2560 52 12573 4.9 1 8503 4070 53 12303 4.9 1 7186 5117 54 6183 4.9 1 4037 2146 55 11114 4.9 1 7729 3385 56 5748 4.9 1 3359 2389 57 6883 4.9 1 4418 2465 58 7876 4.9 1 5099 2777 59 6431 4.9 1 4187 2244 60 8001 4.9 1 5023 2978 61 4195 4.9 1 2878 1317 62 8804 4.9 1 5388 3416 63 3692 4.9 1 2113 1579 64 9232 4.9 1 5099 4133 65 3237 4.9 1 1887 1350 66 7347 4.9 1 4557 2790 67 3312 4.9 1 1722 1590 68 4175 4.9 1 2434 1741 69 3750 4.9 1 2026 1724 70 3785 4.9 1 1876 1909 71 4025 4.9 1 1792 2233 72 4802 4.9 1 1709 3093 73 10517 4.9 1 1982 8535 74 27988 4.9 1 2127 25861 75 65445 4.9 1 2445 63000 76 79593 4.9 1 2799 76794 77 137706 4.9 1 2293 135413 78 153453 4.9 1 2241 151212 79 128136 4.9 1 1354 126782 80 98235 4.9 1 876 97359 81 70344 4.9 1 516 69828 82 49854 4.9 1 374 49480 83 38770 4.9 1 287 38483 84 30921 4.9 1 260 30661 85 29848 4.9 1 218 29630 86 25010 4.9 1 178 24832 87 20835 4.9 1 177 20658 88 17858 4.9 1 133 17725 89 15235 4.9 1 130 15105 90 12452 4.9 1 114 12338 91 10767 4.9 1 90 10677 92 9193 4.9 1 70 9123 93 7733 4.9 1 75 7658 94 6044 4.9 1 68 5976 95 5529 4.9 1 53 5476 96 4814 4.9 1 59 4755 97 4340 4.9 1 47 4293 98 3984 4.9 1 55 3929 99 3463 4.9 1 29 3434 100 3005 4.9 1 49 2956 101 2767 4.9 1 35 2732 102 2648 4.9 1 23 2625 103 2835 4.9 1 35 2800 104 2854 4.9 1 21 2833 105 2959 4.9 1 27 2932 106 3203 4.9 1 35 3168 107 3205 4.9 1 31 3174 108 3357 4.9 1 34 3323 109 3269 4.9 1 28 3241 110 3351 4.9 1 31 3320 111 3397 4.9 1 33 3364 112 3321 4.9 1 38 3283 113 3381 4.9 1 30 3351 114 3063 4.9 1 57 3006 115 2786 4.9 1 24 2762 116 2605 4.9 1 26 2579 117 2304 4.9 1 27 2277 118 2114 4.9 1 27 2087 119 1970 4.9 1 26 1944 120 1733 4.9 1 25 1708 121 1566 4.9 1 27 1539 122 1540 4.9 1 26 1514 123 1383 4.9 1 29 1354 124 1321 4.9 1 30 1291 125 1163 4.9 1 30 1133 126 1120 4.9 1 35 1085 127 987 4.9 1 28 959 128 1013 4.9 1 36 977 129 943 4.9 1 24 919 130 904 4.9 1 24 880 131 875 4.9 1 32 843 132 837 4.9 1 41 796 133 840 4.9 1 39 801 134 796 4.9 1 35 761 135 872 4.9 1 25 847 136 903 4.9 1 37 866 137 848 4.9 1 28 820 138 924 4.9 1 26 898 139 999 4.9 1 25 974 140 1071 4.9 1 26 1045 141 1253 4.9 1 22 1231 142 1424 4.9 1 22 1402 143 1732 4.9 1 22 1710 144 2183 4.9 1 13 2170 145 2983 4.9 1 22 2961 146 4442 4.9 1 21 4421 147 8438 4.9 1 23 8415 148 19945 4.9 1 17 19928 149 33885 4.9 1 5 33880 150 154766 4.9 1 8 154758 151 64351 4.9 1 4 64347 RUN STATISTICS FOR INPUT FILE: juvenile_1.fastq.gz ============================================= 328998671 sequences processed in total