SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 564.66 s (41 us/read; 1.46 M reads/minute). === Summary === Total reads processed: 13,781,290 Reads with adapters: 10,464,679 (75.9%) Reads written (passing filters): 13,781,290 (100.0%) Total basepairs processed: 2,067,193,500 bp Quality-trimmed: 4,066,824 bp (0.2%) Total written (filtered): 1,647,743,968 bp (79.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10464679 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.2% C: 15.6% G: 18.6% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2115194 3445322.5 0 2115194 2 272894 861330.6 0 272894 3 153504 215332.7 0 153504 4 91420 53833.2 0 91420 5 70039 13458.3 0 70039 6 67409 3364.6 0 67409 7 55787 841.1 0 55787 8 69144 210.3 0 69144 9 70298 52.6 0 69211 1087 10 65479 13.1 1 61710 3769 11 71864 3.3 1 66237 5627 12 69709 0.8 1 65113 4596 13 68649 0.2 1 64099 4550 14 71371 0.2 1 66030 5341 15 72335 0.2 1 67349 4986 16 73096 0.2 1 67373 5723 17 87823 0.2 1 80650 7173 18 73513 0.2 1 68795 4718 19 64905 0.2 1 60375 4530 20 76453 0.2 1 71101 5352 21 83756 0.2 1 77496 6260 22 71860 0.2 1 67380 4480 23 82380 0.2 1 76793 5587 24 76931 0.2 1 70531 6400 25 82900 0.2 1 77013 5887 26 75729 0.2 1 70800 4929 27 84549 0.2 1 78103 6446 28 82744 0.2 1 76781 5963 29 87966 0.2 1 80505 7461 30 92743 0.2 1 87256 5487 31 72956 0.2 1 68033 4923 32 86797 0.2 1 81028 5769 33 84425 0.2 1 77963 6462 34 100255 0.2 1 92044 8211 35 94925 0.2 1 87424 7501 36 151403 0.2 1 144008 7395 37 34431 0.2 1 30234 4197 38 81160 0.2 1 76071 5089 39 98494 0.2 1 91430 7064 40 94229 0.2 1 88176 6053 41 105491 0.2 1 97539 7952 42 89350 0.2 1 81822 7528 43 144554 0.2 1 136557 7997 44 52667 0.2 1 48059 4608 45 80312 0.2 1 74870 5442 46 96347 0.2 1 89778 6569 47 100619 0.2 1 94323 6296 48 87690 0.2 1 81510 6180 49 103414 0.2 1 95838 7576 50 86689 0.2 1 81209 5480 51 92177 0.2 1 85927 6250 52 98128 0.2 1 90537 7591 53 111470 0.2 1 104728 6742 54 79643 0.2 1 74106 5537 55 98690 0.2 1 92247 6443 56 114543 0.2 1 107715 6828 57 91001 0.2 1 84632 6369 58 94668 0.2 1 89637 5031 59 73433 0.2 1 68107 5326 60 100893 0.2 1 94469 6424 61 94258 0.2 1 88482 5776 62 93437 0.2 1 87751 5686 63 86189 0.2 1 80341 5848 64 87860 0.2 1 82577 5283 65 95579 0.2 1 89442 6137 66 102630 0.2 1 95991 6639 67 110068 0.2 1 101200 8868 68 211731 0.2 1 201178 10553 69 44241 0.2 1 40907 3334 70 13519 0.2 1 11187 2332 71 49103 0.2 1 45715 3388 72 77796 0.2 1 73169 4627 73 81869 0.2 1 76719 5150 74 82069 0.2 1 76896 5173 75 80967 0.2 1 75833 5134 76 79680 0.2 1 74662 5018 77 80336 0.2 1 75241 5095 78 75811 0.2 1 70973 4838 79 74367 0.2 1 69524 4843 80 73534 0.2 1 69012 4522 81 72214 0.2 1 67540 4674 82 70474 0.2 1 66112 4362 83 68507 0.2 1 64201 4306 84 66184 0.2 1 61986 4198 85 64533 0.2 1 60445 4088 86 62422 0.2 1 58352 4070 87 59642 0.2 1 55842 3800 88 59336 0.2 1 55541 3795 89 56406 0.2 1 52805 3601 90 56172 0.2 1 52495 3677 91 53832 0.2 1 50312 3520 92 51101 0.2 1 47868 3233 93 48168 0.2 1 45095 3073 94 47770 0.2 1 44644 3126 95 44085 0.2 1 41250 2835 96 41623 0.2 1 38858 2765 97 39066 0.2 1 36394 2672 98 35943 0.2 1 33581 2362 99 35291 0.2 1 32748 2543 100 32499 0.2 1 30308 2191 101 30357 0.2 1 28386 1971 102 28530 0.2 1 26552 1978 103 26074 0.2 1 24341 1733 104 24528 0.2 1 22773 1755 105 21898 0.2 1 20353 1545 106 20241 0.2 1 18793 1448 107 18328 0.2 1 16963 1365 108 17608 0.2 1 16339 1269 109 15247 0.2 1 14123 1124 110 14054 0.2 1 12990 1064 111 12816 0.2 1 11851 965 112 11319 0.2 1 10448 871 113 9601 0.2 1 8829 772 114 8785 0.2 1 8065 720 115 7727 0.2 1 7075 652 116 6667 0.2 1 6137 530 117 5842 0.2 1 5341 501 118 5116 0.2 1 4650 466 119 4257 0.2 1 3896 361 120 3744 0.2 1 3400 344 121 3378 0.2 1 3078 300 122 2708 0.2 1 2469 239 123 2529 0.2 1 2246 283 124 2015 0.2 1 1814 201 125 1810 0.2 1 1626 184 126 1647 0.2 1 1490 157 127 1294 0.2 1 1150 144 128 1010 0.2 1 909 101 129 964 0.2 1 860 104 130 736 0.2 1 664 72 131 614 0.2 1 553 61 132 536 0.2 1 487 49 133 628 0.2 1 563 65 134 1415 0.2 1 1342 73 135 608 0.2 1 567 41 136 207 0.2 1 188 19 137 132 0.2 1 118 14 138 84 0.2 1 75 9 139 56 0.2 1 44 12 140 46 0.2 1 36 10 141 40 0.2 1 35 5 142 28 0.2 1 23 5 143 39 0.2 1 32 7 144 49 0.2 1 44 5 145 178 0.2 1 162 16 146 250 0.2 1 233 17 147 1272 0.2 1 1190 82 148 812 0.2 1 771 41 149 417 0.2 1 393 24 150 2828 0.2 1 2398 430 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz ============================================= 13781290 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 10281 (0.1%)