SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L001_R2_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/8C_26psu_4_S12_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 547.67 s (43 us/read; 1.38 M reads/minute). === Summary === Total reads processed: 12,592,704 Reads with adapters: 8,852,263 (70.3%) Reads written (passing filters): 12,592,704 (100.0%) Total basepairs processed: 1,888,905,600 bp Quality-trimmed: 12,948,585 bp (0.7%) Total written (filtered): 1,572,160,709 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8852263 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 12.6% G: 20.6% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2390954 3148176.0 0 2390954 2 298677 787044.0 0 298677 3 170286 196761.0 0 170286 4 88634 49190.2 0 88634 5 67201 12297.6 0 67201 6 54871 3074.4 0 54871 7 42570 768.6 0 42570 8 63033 192.1 0 63033 9 50827 48.0 0 50608 219 10 54798 12.0 1 51719 3079 11 58410 3.0 1 54143 4267 12 59146 0.8 1 54631 4515 13 64024 0.2 1 59760 4264 14 60295 0.2 1 55485 4810 15 48131 0.2 1 44661 3470 16 72030 0.2 1 66991 5039 17 55432 0.2 1 51368 4064 18 54012 0.2 1 50286 3726 19 67964 0.2 1 63040 4924 20 63154 0.2 1 58908 4246 21 56080 0.2 1 52250 3830 22 62812 0.2 1 58598 4214 23 64652 0.2 1 60263 4389 24 64121 0.2 1 59590 4531 25 72378 0.2 1 67726 4652 26 60189 0.2 1 55991 4198 27 67272 0.2 1 62190 5082 28 62061 0.2 1 58469 3592 29 66706 0.2 1 62082 4624 30 64680 0.2 1 60760 3920 31 70875 0.2 1 66272 4603 32 63295 0.2 1 59659 3636 33 68948 0.2 1 64437 4511 34 89723 0.2 1 83808 5915 35 49481 0.2 1 46615 2866 36 69552 0.2 1 64903 4649 37 74271 0.2 1 69458 4813 38 69359 0.2 1 65691 3668 39 67616 0.2 1 63803 3813 40 75243 0.2 1 70372 4871 41 71025 0.2 1 67013 4012 42 73877 0.2 1 69581 4296 43 66995 0.2 1 63092 3903 44 76573 0.2 1 71945 4628 45 80934 0.2 1 76127 4807 46 59833 0.2 1 56439 3394 47 73828 0.2 1 69722 4106 48 73312 0.2 1 69349 3963 49 75078 0.2 1 70776 4302 50 70693 0.2 1 66714 3979 51 88709 0.2 1 83803 4906 52 62743 0.2 1 59451 3292 53 75598 0.2 1 71882 3716 54 57634 0.2 1 54617 3017 55 73802 0.2 1 70193 3609 56 76463 0.2 1 72320 4143 57 71883 0.2 1 68382 3501 58 68729 0.2 1 65597 3132 59 69792 0.2 1 66296 3496 60 72493 0.2 1 68898 3595 61 74181 0.2 1 70431 3750 62 80362 0.2 1 76257 4105 63 105716 0.2 1 100889 4827 64 86565 0.2 1 82909 3656 65 55528 0.2 1 52821 2707 66 61319 0.2 1 58488 2831 67 60096 0.2 1 57177 2919 68 60017 0.2 1 57079 2938 69 59676 0.2 1 56862 2814 70 62200 0.2 1 59177 3023 71 65595 0.2 1 62486 3109 72 62243 0.2 1 59355 2888 73 65321 0.2 1 62407 2914 74 60107 0.2 1 57408 2699 75 56927 0.2 1 54342 2585 76 56197 0.2 1 53642 2555 77 55543 0.2 1 53010 2533 78 53264 0.2 1 50829 2435 79 50917 0.2 1 48532 2385 80 50251 0.2 1 48020 2231 81 49279 0.2 1 47040 2239 82 47377 0.2 1 45259 2118 83 45689 0.2 1 43632 2057 84 44996 0.2 1 42952 2044 85 43197 0.2 1 41186 2011 86 43336 0.2 1 41365 1971 87 42821 0.2 1 40993 1828 88 42339 0.2 1 40455 1884 89 37924 0.2 1 36191 1733 90 36727 0.2 1 35019 1708 91 33632 0.2 1 32108 1524 92 32065 0.2 1 30559 1506 93 30818 0.2 1 29434 1384 94 30025 0.2 1 28706 1319 95 28433 0.2 1 27167 1266 96 27472 0.2 1 26315 1157 97 25080 0.2 1 23956 1124 98 23110 0.2 1 22057 1053 99 21635 0.2 1 20659 976 100 19482 0.2 1 18587 895 101 17939 0.2 1 17090 849 102 17260 0.2 1 16487 773 103 15967 0.2 1 15237 730 104 15618 0.2 1 14883 735 105 13954 0.2 1 13334 620 106 12766 0.2 1 12218 548 107 11338 0.2 1 10826 512 108 10218 0.2 1 9719 499 109 9371 0.2 1 8900 471 110 8643 0.2 1 8250 393 111 8343 0.2 1 7959 384 112 7194 0.2 1 6837 357 113 6183 0.2 1 5873 310 114 5369 0.2 1 5131 238 115 4668 0.2 1 4438 230 116 3833 0.2 1 3644 189 117 3219 0.2 1 3007 212 118 2818 0.2 1 2669 149 119 2453 0.2 1 2312 141 120 2060 0.2 1 1936 124 121 1912 0.2 1 1802 110 122 1619 0.2 1 1536 83 123 1396 0.2 1 1315 81 124 1132 0.2 1 1057 75 125 1047 0.2 1 976 71 126 972 0.2 1 915 57 127 819 0.2 1 758 61 128 624 0.2 1 581 43 129 486 0.2 1 450 36 130 458 0.2 1 430 28 131 510 0.2 1 482 28 132 584 0.2 1 562 22 133 1105 0.2 1 1055 50 134 2683 0.2 1 2615 68 135 802 0.2 1 778 24 136 171 0.2 1 159 12 137 100 0.2 1 93 7 138 80 0.2 1 73 7 139 45 0.2 1 40 5 140 54 0.2 1 48 6 141 22 0.2 1 17 5 142 19 0.2 1 18 1 143 19 0.2 1 16 3 144 60 0.2 1 57 3 145 202 0.2 1 195 7 146 219 0.2 1 210 9 147 1124 0.2 1 1091 33 148 721 0.2 1 692 29 149 428 0.2 1 410 18 150 2417 0.2 1 2310 107 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L001_R2_001.fastq.gz ============================================= 12592704 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 31314 (0.2%)