SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_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_26psu_3_S11_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 629.90 s (37 us/read; 1.64 M reads/minute). === Summary === Total reads processed: 17,221,011 Reads with adapters: 14,907,348 (86.6%) Reads written (passing filters): 17,221,011 (100.0%) Total basepairs processed: 2,583,151,650 bp Quality-trimmed: 4,970,961 bp (0.2%) Total written (filtered): 1,823,787,303 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14907348 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 14.0% G: 22.2% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1339401 4305252.8 0 1339401 2 221513 1076313.2 0 221513 3 135887 269078.3 0 135887 4 86877 67269.6 0 86877 5 77129 16817.4 0 77129 6 76711 4204.3 0 76711 7 64192 1051.1 0 64192 8 80722 262.8 0 80722 9 81072 65.7 0 80149 923 10 77051 16.4 1 73224 3827 11 85961 4.1 1 79699 6262 12 83198 1.0 1 78237 4961 13 86825 0.3 1 81365 5460 14 84806 0.3 1 79388 5418 15 92317 0.3 1 86654 5663 16 89335 0.3 1 83153 6182 17 108017 0.3 1 99755 8262 18 99925 0.3 1 94377 5548 19 81101 0.3 1 76294 4807 20 100416 0.3 1 94250 6166 21 108388 0.3 1 101446 6942 22 94203 0.3 1 89329 4874 23 109171 0.3 1 102371 6800 24 104496 0.3 1 96618 7878 25 111703 0.3 1 104639 7064 26 103882 0.3 1 98042 5840 27 115801 0.3 1 107736 8065 28 113315 0.3 1 105981 7334 29 122732 0.3 1 113578 9154 30 129896 0.3 1 123034 6862 31 104938 0.3 1 98897 6041 32 124822 0.3 1 117479 7343 33 120235 0.3 1 112658 7577 34 135691 0.3 1 125410 10281 35 143924 0.3 1 135732 8192 36 114731 0.3 1 107772 6959 37 138113 0.3 1 128706 9407 38 183834 0.3 1 174741 9093 39 91269 0.3 1 83934 7335 40 144200 0.3 1 135345 8855 41 167039 0.3 1 155843 11196 42 124510 0.3 1 116014 8496 43 229902 0.3 1 218995 10907 44 61751 0.3 1 56507 5244 45 153093 0.3 1 144067 9026 46 145804 0.3 1 137245 8559 47 154404 0.3 1 145632 8772 48 154492 0.3 1 145156 9336 49 169124 0.3 1 158402 10722 50 144085 0.3 1 136047 8038 51 159010 0.3 1 149344 9666 52 165606 0.3 1 154687 10919 53 178026 0.3 1 167943 10083 54 145073 0.3 1 136817 8256 55 172012 0.3 1 161558 10454 56 210944 0.3 1 199588 11356 57 131803 0.3 1 123033 8770 58 178194 0.3 1 169188 9006 59 157761 0.3 1 148537 9224 60 170653 0.3 1 160454 10199 61 170629 0.3 1 161244 9385 62 190264 0.3 1 180168 10096 63 148311 0.3 1 139056 9255 64 170495 0.3 1 161109 9386 65 191349 0.3 1 180352 10997 66 199623 0.3 1 188220 11403 67 212270 0.3 1 197036 15234 68 412894 0.3 1 394953 17941 69 59319 0.3 1 54157 5162 70 23953 0.3 1 19703 4250 71 116809 0.3 1 110410 6399 72 157277 0.3 1 148914 8363 73 165912 0.3 1 156892 9020 74 164518 0.3 1 155310 9208 75 163178 0.3 1 154082 9096 76 162323 0.3 1 153580 8743 77 162174 0.3 1 153149 9025 78 154081 0.3 1 145262 8819 79 153448 0.3 1 144767 8681 80 149998 0.3 1 141770 8228 81 150056 0.3 1 141671 8385 82 147165 0.3 1 139005 8160 83 142399 0.3 1 134518 7881 84 137532 0.3 1 129880 7652 85 134287 0.3 1 126887 7400 86 129443 0.3 1 122227 7216 87 125510 0.3 1 118421 7089 88 124525 0.3 1 117462 7063 89 118345 0.3 1 111665 6680 90 118308 0.3 1 111670 6638 91 111912 0.3 1 105689 6223 92 106445 0.3 1 100472 5973 93 100557 0.3 1 94827 5730 94 97750 0.3 1 92088 5662 95 91346 0.3 1 86041 5305 96 86885 0.3 1 81735 5150 97 81399 0.3 1 76644 4755 98 75784 0.3 1 71395 4389 99 72904 0.3 1 68310 4594 100 67617 0.3 1 63610 4007 101 63261 0.3 1 59615 3646 102 58086 0.3 1 54536 3550 103 54397 0.3 1 51127 3270 104 50493 0.3 1 47351 3142 105 44481 0.3 1 41579 2902 106 41013 0.3 1 38506 2507 107 36987 0.3 1 34603 2384 108 34766 0.3 1 32511 2255 109 30744 0.3 1 28764 1980 110 27509 0.3 1 25598 1911 111 24797 0.3 1 23127 1670 112 21804 0.3 1 20294 1510 113 18744 0.3 1 17435 1309 114 16804 0.3 1 15658 1146 115 14315 0.3 1 13251 1064 116 12612 0.3 1 11627 985 117 10473 0.3 1 9684 789 118 8921 0.3 1 8216 705 119 7563 0.3 1 6922 641 120 6332 0.3 1 5781 551 121 5619 0.3 1 5122 497 122 4576 0.3 1 4198 378 123 3737 0.3 1 3370 367 124 3104 0.3 1 2823 281 125 2623 0.3 1 2320 303 126 2119 0.3 1 1927 192 127 1819 0.3 1 1640 179 128 1359 0.3 1 1208 151 129 1165 0.3 1 1033 132 130 852 0.3 1 749 103 131 856 0.3 1 765 91 132 726 0.3 1 633 93 133 874 0.3 1 793 81 134 1491 0.3 1 1401 90 135 611 0.3 1 548 63 136 207 0.3 1 187 20 137 166 0.3 1 155 11 138 132 0.3 1 107 25 139 75 0.3 1 67 8 140 69 0.3 1 60 9 141 42 0.3 1 32 10 142 26 0.3 1 19 7 143 26 0.3 1 15 11 144 18 0.3 1 13 5 145 37 0.3 1 33 4 146 26 0.3 1 20 6 147 73 0.3 1 60 13 148 47 0.3 1 37 10 149 55 0.3 1 48 7 150 636 0.3 1 548 88 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L001_R1_001.fastq.gz ============================================= 17221011 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 6252 (0.0%)