SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_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/CTRL_16C_26psu_1_S19_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 763.05 s (41 us/read; 1.45 M reads/minute). === Summary === Total reads processed: 18,490,322 Reads with adapters: 14,542,227 (78.6%) Reads written (passing filters): 18,490,322 (100.0%) Total basepairs processed: 2,773,548,300 bp Quality-trimmed: 5,682,539 bp (0.2%) Total written (filtered): 2,170,540,982 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14542227 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.1% G: 20.7% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2352565 4622580.5 0 2352565 2 355744 1155645.1 0 355744 3 197435 288911.3 0 197435 4 119803 72227.8 0 119803 5 101491 18057.0 0 101491 6 98683 4514.2 0 98683 7 82227 1128.6 0 82227 8 107087 282.1 0 107087 9 96108 70.5 0 94984 1124 10 95916 17.6 1 89656 6260 11 105518 4.4 1 96331 9187 12 101326 1.1 1 93731 7595 13 105529 0.3 1 97295 8234 14 104207 0.3 1 95707 8500 15 110166 0.3 1 101496 8670 16 108369 0.3 1 98900 9469 17 132137 0.3 1 119869 12268 18 111785 0.3 1 103776 8009 19 94978 0.3 1 88024 6954 20 115852 0.3 1 107171 8681 21 128602 0.3 1 118248 10354 22 106928 0.3 1 99662 7266 23 130246 0.3 1 120393 9853 24 113598 0.3 1 103348 10250 25 127529 0.3 1 117557 9972 26 114329 0.3 1 106365 7964 27 127671 0.3 1 117117 10554 28 133545 0.3 1 122886 10659 29 127218 0.3 1 116368 10850 30 145807 0.3 1 136218 9589 31 104710 0.3 1 97327 7383 32 136712 0.3 1 126029 10683 33 125051 0.3 1 114983 10068 34 151172 0.3 1 138255 12917 35 121506 0.3 1 112294 9212 36 142450 0.3 1 131732 10718 37 131704 0.3 1 122359 9345 38 144055 0.3 1 132700 11355 39 140259 0.3 1 129402 10857 40 145119 0.3 1 132998 12121 41 151317 0.3 1 136837 14480 42 135755 0.3 1 124185 11570 43 206150 0.3 1 193096 13054 44 75981 0.3 1 68776 7205 45 147101 0.3 1 136563 10538 46 140010 0.3 1 129569 10441 47 150202 0.3 1 139726 10476 48 137985 0.3 1 127406 10579 49 157361 0.3 1 144848 12513 50 132126 0.3 1 123324 8802 51 143254 0.3 1 133169 10085 52 152534 0.3 1 140225 12309 53 166653 0.3 1 155543 11110 54 122896 0.3 1 113877 9019 55 150505 0.3 1 139851 10654 56 178712 0.3 1 166946 11766 57 130999 0.3 1 120759 10240 58 145047 0.3 1 136344 8703 59 119684 0.3 1 110878 8806 60 151206 0.3 1 140682 10524 61 142715 0.3 1 133251 9464 62 148943 0.3 1 139114 9829 63 129912 0.3 1 120416 9496 64 134038 0.3 1 125474 8564 65 146595 0.3 1 136655 9940 66 153978 0.3 1 143441 10537 67 168100 0.3 1 155171 12929 68 298170 0.3 1 281868 16302 69 74393 0.3 1 68405 5988 70 26909 0.3 1 22880 4029 71 75109 0.3 1 70102 5007 72 114931 0.3 1 107946 6985 73 122734 0.3 1 114818 7916 74 120820 0.3 1 112962 7858 75 119099 0.3 1 111010 8089 76 117029 0.3 1 108855 8174 77 117800 0.3 1 109726 8074 78 109388 0.3 1 101815 7573 79 108107 0.3 1 100589 7518 80 105715 0.3 1 98229 7486 81 104556 0.3 1 97305 7251 82 101011 0.3 1 93996 7015 83 97159 0.3 1 90577 6582 84 92283 0.3 1 85890 6393 85 90035 0.3 1 83799 6236 86 86319 0.3 1 80378 5941 87 82376 0.3 1 76893 5483 88 81375 0.3 1 75753 5622 89 77211 0.3 1 71720 5491 90 76508 0.3 1 71173 5335 91 72845 0.3 1 67788 5057 92 67776 0.3 1 63180 4596 93 63675 0.3 1 59371 4304 94 61289 0.3 1 57047 4242 95 57075 0.3 1 53036 4039 96 54087 0.3 1 50327 3760 97 51019 0.3 1 47507 3512 98 46423 0.3 1 43108 3315 99 45164 0.3 1 41742 3422 100 40910 0.3 1 38024 2886 101 38601 0.3 1 35925 2676 102 35185 0.3 1 32582 2603 103 32331 0.3 1 30034 2297 104 30306 0.3 1 28179 2127 105 26497 0.3 1 24651 1846 106 24125 0.3 1 22458 1667 107 22000 0.3 1 20417 1583 108 20719 0.3 1 19189 1530 109 18051 0.3 1 16712 1339 110 16439 0.3 1 15194 1245 111 14466 0.3 1 13407 1059 112 12793 0.3 1 11768 1025 113 11344 0.3 1 10481 863 114 9637 0.3 1 8889 748 115 8596 0.3 1 7840 756 116 7497 0.3 1 6926 571 117 6216 0.3 1 5692 524 118 5413 0.3 1 4943 470 119 4488 0.3 1 4121 367 120 3934 0.3 1 3598 336 121 3277 0.3 1 2991 286 122 2701 0.3 1 2461 240 123 2240 0.3 1 2028 212 124 1944 0.3 1 1730 214 125 1578 0.3 1 1422 156 126 1320 0.3 1 1199 121 127 1172 0.3 1 1056 116 128 861 0.3 1 773 88 129 759 0.3 1 683 76 130 595 0.3 1 520 75 131 487 0.3 1 426 61 132 384 0.3 1 352 32 133 353 0.3 1 318 35 134 434 0.3 1 399 35 135 273 0.3 1 245 28 136 156 0.3 1 137 19 137 94 0.3 1 83 11 138 77 0.3 1 69 8 139 51 0.3 1 44 7 140 30 0.3 1 25 5 141 33 0.3 1 24 9 142 30 0.3 1 24 6 143 35 0.3 1 27 8 144 18 0.3 1 17 1 145 11 0.3 1 9 2 146 25 0.3 1 21 4 147 75 0.3 1 73 2 148 42 0.3 1 37 5 149 44 0.3 1 41 3 150 294 0.3 1 257 37 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_L002_R1_001.fastq.gz ============================================= 18490322 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3001 (0.0%)