SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_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_4_S8_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 614.41 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 14,686,084 Reads with adapters: 11,112,819 (75.7%) Reads written (passing filters): 14,686,084 (100.0%) Total basepairs processed: 2,202,912,600 bp Quality-trimmed: 9,079,514 bp (0.4%) Total written (filtered): 1,783,990,340 bp (81.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11112819 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 11.7% G: 21.0% T: 36.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2196567 3671521.0 0 2196567 2 292186 917880.2 0 292186 3 157941 229470.1 0 157941 4 100753 57367.5 0 100753 5 83202 14341.9 0 83202 6 81280 3585.5 0 81280 7 68619 896.4 0 68619 8 84673 224.1 0 84673 9 83412 56.0 0 82605 807 10 77900 14.0 1 74163 3737 11 86076 3.5 1 80161 5915 12 82933 0.9 1 78087 4846 13 83856 0.2 1 78977 4879 14 84709 0.2 1 79208 5501 15 88097 0.2 1 82938 5159 16 88174 0.2 1 82008 6166 17 105389 0.2 1 97630 7759 18 89620 0.2 1 84611 5009 19 77413 0.2 1 72875 4538 20 91427 0.2 1 86037 5390 21 101267 0.2 1 94618 6649 22 86534 0.2 1 82143 4391 23 99603 0.2 1 93638 5965 24 92844 0.2 1 85594 7250 25 98567 0.2 1 92532 6035 26 89487 0.2 1 84719 4768 27 100312 0.2 1 93524 6788 28 97676 0.2 1 91379 6297 29 103869 0.2 1 95980 7889 30 115073 0.2 1 109144 5929 31 81679 0.2 1 76971 4708 32 104832 0.2 1 98556 6276 33 97135 0.2 1 91030 6105 34 104303 0.2 1 98156 6147 35 102079 0.2 1 95269 6810 36 105105 0.2 1 98314 6791 37 106489 0.2 1 100050 6439 38 111587 0.2 1 104304 7283 39 98240 0.2 1 93162 5078 40 110224 0.2 1 103236 6988 41 119138 0.2 1 109010 10128 42 107751 0.2 1 99258 8493 43 167048 0.2 1 157990 9058 44 54792 0.2 1 50043 4749 45 116148 0.2 1 107107 9041 46 253343 0.2 1 239166 14177 47 141220 0.2 1 133245 7975 48 70788 0.2 1 63989 6799 49 218187 0.2 1 207304 10883 50 67793 0.2 1 62869 4924 51 84957 0.2 1 78961 5996 52 231141 0.2 1 220209 10932 53 159552 0.2 1 153244 6308 54 57820 0.2 1 54077 3743 55 96525 0.2 1 92498 4027 56 56201 0.2 1 52298 3903 57 134736 0.2 1 129198 5538 58 33322 0.2 1 31241 2081 59 35361 0.2 1 32301 3060 60 121909 0.2 1 116692 5217 61 80368 0.2 1 77075 3293 62 37240 0.2 1 34469 2771 63 91660 0.2 1 86780 4880 64 81468 0.2 1 77877 3591 65 53211 0.2 1 49893 3318 66 93831 0.2 1 88616 5215 67 107034 0.2 1 100335 6699 68 187851 0.2 1 179197 8654 69 100255 0.2 1 94892 5363 70 35399 0.2 1 32342 3057 71 19897 0.2 1 17997 1900 72 63849 0.2 1 60613 3236 73 81267 0.2 1 77051 4216 74 82339 0.2 1 77944 4395 75 80643 0.2 1 76099 4544 76 79016 0.2 1 74790 4226 77 78401 0.2 1 74108 4293 78 73966 0.2 1 69851 4115 79 71627 0.2 1 67584 4043 80 70426 0.2 1 66563 3863 81 69818 0.2 1 65954 3864 82 67366 0.2 1 63575 3791 83 63649 0.2 1 60193 3456 84 61172 0.2 1 57824 3348 85 59276 0.2 1 56040 3236 86 56575 0.2 1 53454 3121 87 53078 0.2 1 50236 2842 88 51788 0.2 1 48829 2959 89 48314 0.2 1 45638 2676 90 48321 0.2 1 45629 2692 91 45543 0.2 1 43073 2470 92 42075 0.2 1 39779 2296 93 38814 0.2 1 36658 2156 94 37722 0.2 1 35616 2106 95 34423 0.2 1 32423 2000 96 32157 0.2 1 30284 1873 97 29965 0.2 1 28206 1759 98 27347 0.2 1 25797 1550 99 26166 0.2 1 24583 1583 100 23354 0.2 1 21969 1385 101 21467 0.2 1 20157 1310 102 19539 0.2 1 18344 1195 103 17855 0.2 1 16735 1120 104 16360 0.2 1 15329 1031 105 14296 0.2 1 13369 927 106 12633 0.2 1 11870 763 107 11358 0.2 1 10612 746 108 10534 0.2 1 9836 698 109 9078 0.2 1 8461 617 110 8053 0.2 1 7464 589 111 6944 0.2 1 6454 490 112 6153 0.2 1 5691 462 113 5306 0.2 1 4906 400 114 4518 0.2 1 4189 329 115 3910 0.2 1 3603 307 116 3193 0.2 1 2951 242 117 2651 0.2 1 2439 212 118 2314 0.2 1 2103 211 119 1875 0.2 1 1673 202 120 1577 0.2 1 1427 150 121 1320 0.2 1 1198 122 122 1105 0.2 1 995 110 123 920 0.2 1 816 104 124 791 0.2 1 709 82 125 642 0.2 1 583 59 126 507 0.2 1 450 57 127 422 0.2 1 367 55 128 333 0.2 1 289 44 129 238 0.2 1 206 32 130 186 0.2 1 162 24 131 174 0.2 1 151 23 132 134 0.2 1 118 16 133 148 0.2 1 129 19 134 197 0.2 1 182 15 135 113 0.2 1 97 16 136 58 0.2 1 50 8 137 58 0.2 1 48 10 138 42 0.2 1 35 7 139 30 0.2 1 28 2 140 22 0.2 1 20 2 141 15 0.2 1 9 6 142 13 0.2 1 11 2 143 11 0.2 1 6 5 144 2 0.2 1 1 1 145 7 0.2 1 6 1 146 5 0.2 1 4 1 147 21 0.2 1 20 1 148 23 0.2 1 19 4 149 14 0.2 1 12 2 150 119 0.2 1 95 24 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L001_R1_001.fastq.gz ============================================= 14686084 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1248 (0.0%)