SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_3_S3_L002_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/16C_32psu_3_S3_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 510.86 s (37 us/read; 1.61 M reads/minute). === Summary === Total reads processed: 13,670,957 Reads with adapters: 11,663,120 (85.3%) Reads written (passing filters): 13,670,957 (100.0%) Total basepairs processed: 2,050,643,550 bp Quality-trimmed: 4,231,959 bp (0.2%) Total written (filtered): 1,462,745,020 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11663120 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 13.5% G: 21.8% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1152864 3417739.2 0 1152864 2 186575 854434.8 0 186575 3 110892 213608.7 0 110892 4 68686 53402.2 0 68686 5 61523 13350.5 0 61523 6 61066 3337.6 0 61066 7 49563 834.4 0 49563 8 63725 208.6 0 63725 9 62710 52.2 0 61945 765 10 59136 13.0 1 55273 3863 11 67741 3.3 1 61750 5991 12 63923 0.8 1 59045 4878 13 66568 0.2 1 61427 5141 14 66808 0.2 1 61285 5523 15 71031 0.2 1 65247 5784 16 70289 0.2 1 63984 6305 17 86030 0.2 1 77755 8275 18 73739 0.2 1 68290 5449 19 63306 0.2 1 58569 4737 20 77355 0.2 1 71402 5953 21 85573 0.2 1 78654 6919 22 72710 0.2 1 67584 5126 23 86414 0.2 1 79515 6899 24 79027 0.2 1 71591 7436 25 86879 0.2 1 79866 7013 26 79473 0.2 1 73820 5653 27 90733 0.2 1 83035 7698 28 90102 0.2 1 83123 6979 29 92865 0.2 1 84237 8628 30 100457 0.2 1 93462 6995 31 79802 0.2 1 73917 5885 32 97719 0.2 1 90137 7582 33 93085 0.2 1 85177 7908 34 99262 0.2 1 90786 8476 35 104947 0.2 1 96795 8152 36 99380 0.2 1 91895 7485 37 106441 0.2 1 96879 9562 38 114379 0.2 1 105498 8881 39 96631 0.2 1 89100 7531 40 112490 0.2 1 103151 9339 41 123125 0.2 1 112471 10654 42 98677 0.2 1 90013 8664 43 172897 0.2 1 162100 10797 44 52704 0.2 1 47226 5478 45 117558 0.2 1 108914 8644 46 110418 0.2 1 102198 8220 47 119359 0.2 1 110565 8794 48 116841 0.2 1 108072 8769 49 129611 0.2 1 119238 10373 50 111895 0.2 1 104242 7653 51 123193 0.2 1 114083 9110 52 127566 0.2 1 117108 10458 53 137342 0.2 1 127459 9883 54 110167 0.2 1 102021 8146 55 130673 0.2 1 120967 9706 56 160643 0.2 1 149587 11056 57 104913 0.2 1 96311 8602 58 136727 0.2 1 128029 8698 59 118611 0.2 1 109706 8905 60 133859 0.2 1 123864 9995 61 131656 0.2 1 122381 9275 62 147218 0.2 1 137094 10124 63 117137 0.2 1 107812 9325 64 130610 0.2 1 121719 8891 65 145884 0.2 1 135248 10636 66 150729 0.2 1 139945 10784 67 163505 0.2 1 149584 13921 68 306709 0.2 1 289681 17028 69 62043 0.2 1 56562 5481 70 23965 0.2 1 19784 4181 71 84291 0.2 1 78568 5723 72 119692 0.2 1 111910 7782 73 127200 0.2 1 118724 8476 74 126943 0.2 1 118057 8886 75 127010 0.2 1 118252 8758 76 125373 0.2 1 116194 9179 77 125254 0.2 1 116388 8866 78 119533 0.2 1 110788 8745 79 118816 0.2 1 110233 8583 80 116241 0.2 1 107681 8560 81 114798 0.2 1 106595 8203 82 112468 0.2 1 104279 8189 83 109667 0.2 1 101888 7779 84 105890 0.2 1 98240 7650 85 103302 0.2 1 95804 7498 86 101064 0.2 1 93722 7342 87 97500 0.2 1 90687 6813 88 96898 0.2 1 89881 7017 89 91450 0.2 1 84968 6482 90 91495 0.2 1 84920 6575 91 86388 0.2 1 80232 6156 92 82291 0.2 1 76556 5735 93 78431 0.2 1 72788 5643 94 75874 0.2 1 70339 5535 95 70751 0.2 1 65675 5076 96 67352 0.2 1 62368 4984 97 63954 0.2 1 59443 4511 98 58850 0.2 1 54439 4411 99 58771 0.2 1 54248 4523 100 52467 0.2 1 48655 3812 101 49569 0.2 1 45811 3758 102 45464 0.2 1 42074 3390 103 41939 0.2 1 38904 3035 104 39055 0.2 1 36189 2866 105 34942 0.2 1 32296 2646 106 31969 0.2 1 29559 2410 107 29286 0.2 1 27065 2221 108 27282 0.2 1 25136 2146 109 24507 0.2 1 22544 1963 110 21811 0.2 1 20137 1674 111 19775 0.2 1 18232 1543 112 17157 0.2 1 15740 1417 113 14815 0.2 1 13543 1272 114 13327 0.2 1 12234 1093 115 11366 0.2 1 10408 958 116 9845 0.2 1 9004 841 117 8405 0.2 1 7663 742 118 7384 0.2 1 6703 681 119 6035 0.2 1 5477 558 120 4910 0.2 1 4438 472 121 4090 0.2 1 3702 388 122 3634 0.2 1 3283 351 123 3044 0.2 1 2741 303 124 2552 0.2 1 2281 271 125 2030 0.2 1 1827 203 126 1757 0.2 1 1559 198 127 1362 0.2 1 1204 158 128 1097 0.2 1 981 116 129 1002 0.2 1 874 128 130 785 0.2 1 685 100 131 638 0.2 1 562 76 132 540 0.2 1 480 60 133 462 0.2 1 415 47 134 556 0.2 1 494 62 135 352 0.2 1 314 38 136 204 0.2 1 176 28 137 149 0.2 1 133 16 138 114 0.2 1 99 15 139 71 0.2 1 62 9 140 64 0.2 1 52 12 141 32 0.2 1 25 7 142 45 0.2 1 42 3 143 51 0.2 1 43 8 144 31 0.2 1 25 6 145 45 0.2 1 31 14 146 90 0.2 1 77 13 147 226 0.2 1 201 25 148 203 0.2 1 185 18 149 84 0.2 1 77 7 150 819 0.2 1 651 168 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_3_S3_L002_R1_001.fastq.gz ============================================= 13670957 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 4822 (0.0%)