SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_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/8C_32psu_2_S6_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 511.85 s (40 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 12,939,154 Reads with adapters: 10,340,662 (79.9%) Reads written (passing filters): 12,939,154 (100.0%) Total basepairs processed: 1,940,873,100 bp Quality-trimmed: 3,580,813 bp (0.2%) Total written (filtered): 1,492,993,480 bp (76.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10340662 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 14.7% G: 20.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1552261 3234788.5 0 1552261 2 232662 808697.1 0 232662 3 131614 202174.3 0 131614 4 79987 50543.6 0 79987 5 67280 12635.9 0 67280 6 66472 3159.0 0 66472 7 55108 789.7 0 55108 8 68928 197.4 0 68928 9 68982 49.4 0 68109 873 10 64214 12.3 1 60894 3320 11 72301 3.1 1 66989 5312 12 69430 0.8 1 65113 4317 13 71580 0.2 1 67020 4560 14 70477 0.2 1 65870 4607 15 75676 0.2 1 70785 4891 16 72936 0.2 1 67871 5065 17 87298 0.2 1 80460 6838 18 79611 0.2 1 74935 4676 19 65534 0.2 1 61501 4033 20 79604 0.2 1 74644 4960 21 85256 0.2 1 79605 5651 22 73838 0.2 1 69798 4040 23 84971 0.2 1 79628 5343 24 80676 0.2 1 74456 6220 25 85904 0.2 1 80404 5500 26 79805 0.2 1 75204 4601 27 88623 0.2 1 82274 6349 28 86173 0.2 1 80506 5667 29 91469 0.2 1 84355 7114 30 95793 0.2 1 90568 5225 31 77688 0.2 1 72851 4837 32 92600 0.2 1 86938 5662 33 87750 0.2 1 82121 5629 34 99316 0.2 1 92291 7025 35 87021 0.2 1 82303 4718 36 99065 0.2 1 92449 6616 37 101447 0.2 1 95128 6319 38 97080 0.2 1 90884 6196 39 103846 0.2 1 96530 7316 40 94829 0.2 1 89475 5354 41 105310 0.2 1 97483 7827 42 95966 0.2 1 89196 6770 43 151686 0.2 1 144208 7478 44 46892 0.2 1 42892 4000 45 105867 0.2 1 99520 6347 46 96566 0.2 1 90512 6054 47 103096 0.2 1 97153 5943 48 102489 0.2 1 96145 6344 49 112243 0.2 1 104909 7334 50 94609 0.2 1 89107 5502 51 103165 0.2 1 96761 6404 52 107310 0.2 1 100073 7237 53 113172 0.2 1 106618 6554 54 92162 0.2 1 86748 5414 55 108541 0.2 1 101655 6886 56 133677 0.2 1 126253 7424 57 81980 0.2 1 76375 5605 58 110163 0.2 1 104385 5778 59 98316 0.2 1 92340 5976 60 104988 0.2 1 98449 6539 61 103910 0.2 1 97861 6049 62 115389 0.2 1 108890 6499 63 89259 0.2 1 83482 5777 64 102584 0.2 1 96877 5707 65 114383 0.2 1 107700 6683 66 118785 0.2 1 111674 7111 67 124927 0.2 1 115790 9137 68 236831 0.2 1 226263 10568 69 32490 0.2 1 29503 2987 70 14743 0.2 1 12126 2617 71 68006 0.2 1 64211 3795 72 89001 0.2 1 84078 4923 73 92459 0.2 1 87195 5264 74 91411 0.2 1 86036 5375 75 90970 0.2 1 85629 5341 76 89709 0.2 1 84538 5171 77 89140 0.2 1 84081 5059 78 83843 0.2 1 78811 5032 79 83141 0.2 1 78204 4937 80 80837 0.2 1 76149 4688 81 79618 0.2 1 74844 4774 82 77902 0.2 1 73376 4526 83 75605 0.2 1 71189 4416 84 73149 0.2 1 68920 4229 85 70442 0.2 1 66393 4049 86 67311 0.2 1 63325 3986 87 65584 0.2 1 61688 3896 88 63773 0.2 1 60070 3703 89 60201 0.2 1 56655 3546 90 59708 0.2 1 56173 3535 91 56748 0.2 1 53363 3385 92 53671 0.2 1 50489 3182 93 50670 0.2 1 47624 3046 94 48704 0.2 1 45782 2922 95 45200 0.2 1 42460 2740 96 42497 0.2 1 39903 2594 97 39947 0.2 1 37451 2496 98 36683 0.2 1 34398 2285 99 36692 0.2 1 34265 2427 100 32868 0.2 1 30853 2015 101 30512 0.2 1 28489 2023 102 27906 0.2 1 26115 1791 103 26175 0.2 1 24518 1657 104 23983 0.2 1 22398 1585 105 21704 0.2 1 20274 1430 106 19667 0.2 1 18358 1309 107 17851 0.2 1 16610 1241 108 16494 0.2 1 15292 1202 109 14962 0.2 1 13856 1106 110 13424 0.2 1 12418 1006 111 12110 0.2 1 11218 892 112 10668 0.2 1 9941 727 113 8879 0.2 1 8200 679 114 7950 0.2 1 7388 562 115 7058 0.2 1 6505 553 116 6198 0.2 1 5702 496 117 5071 0.2 1 4638 433 118 4567 0.2 1 4226 341 119 3829 0.2 1 3494 335 120 3187 0.2 1 2901 286 121 2891 0.2 1 2612 279 122 2303 0.2 1 2110 193 123 1890 0.2 1 1705 185 124 1701 0.2 1 1504 197 125 1363 0.2 1 1208 155 126 1199 0.2 1 1086 113 127 954 0.2 1 859 95 128 812 0.2 1 702 110 129 610 0.2 1 539 71 130 529 0.2 1 472 57 131 405 0.2 1 354 51 132 324 0.2 1 279 45 133 284 0.2 1 248 36 134 306 0.2 1 272 34 135 179 0.2 1 161 18 136 123 0.2 1 97 26 137 92 0.2 1 81 11 138 74 0.2 1 60 14 139 42 0.2 1 38 4 140 25 0.2 1 20 5 141 21 0.2 1 16 5 142 15 0.2 1 14 1 143 11 0.2 1 8 3 144 7 0.2 1 5 2 145 18 0.2 1 14 4 146 10 0.2 1 8 2 147 32 0.2 1 32 148 16 0.2 1 16 149 9 0.2 1 5 4 150 128 0.2 1 105 23 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_L001_R1_001.fastq.gz ============================================= 12939154 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2164 (0.0%)