SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_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/CTRL_16C_26psu_1_S19_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 755.53 s (41 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 18,576,202 Reads with adapters: 14,608,493 (78.6%) Reads written (passing filters): 18,576,202 (100.0%) Total basepairs processed: 2,786,430,300 bp Quality-trimmed: 5,505,335 bp (0.2%) Total written (filtered): 2,183,212,736 bp (78.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14608493 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 14.1% G: 20.7% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2367687 4644050.5 0 2367687 2 362390 1161012.6 0 362390 3 199560 290253.2 0 199560 4 122411 72563.3 0 122411 5 101824 18140.8 0 101824 6 98694 4535.2 0 98694 7 85930 1133.8 0 85930 8 108616 283.5 0 108616 9 98214 70.9 0 96968 1246 10 98262 17.7 1 93000 5262 11 106716 4.4 1 98716 8000 12 102761 1.1 1 96030 6731 13 106394 0.3 1 99361 7033 14 105192 0.3 1 97880 7312 15 111384 0.3 1 104056 7328 16 109489 0.3 1 101402 8087 17 132410 0.3 1 121978 10432 18 113576 0.3 1 106813 6763 19 98216 0.3 1 92113 6103 20 116366 0.3 1 109085 7281 21 128770 0.3 1 119833 8937 22 109971 0.3 1 103795 6176 23 129883 0.3 1 121543 8340 24 115035 0.3 1 105774 9261 25 127548 0.3 1 119043 8505 26 115805 0.3 1 109020 6785 27 128062 0.3 1 118816 9246 28 133464 0.3 1 123994 9470 29 128355 0.3 1 118623 9732 30 145787 0.3 1 137741 8046 31 107347 0.3 1 100584 6763 32 136432 0.3 1 127704 8728 33 126911 0.3 1 118459 8452 34 150928 0.3 1 140208 10720 35 123580 0.3 1 115931 7649 36 142531 0.3 1 133504 9027 37 133143 0.3 1 125509 7634 38 143413 0.3 1 133925 9488 39 142038 0.3 1 132863 9175 40 145926 0.3 1 136263 9663 41 151709 0.3 1 139050 12659 42 137644 0.3 1 127697 9947 43 208996 0.3 1 198310 10686 44 73738 0.3 1 67589 6149 45 147037 0.3 1 138219 8818 46 140744 0.3 1 131869 8875 47 152223 0.3 1 143116 9107 48 139803 0.3 1 130633 9170 49 156282 0.3 1 145534 10748 50 133834 0.3 1 126283 7551 51 143388 0.3 1 134512 8876 52 151003 0.3 1 140213 10790 53 166892 0.3 1 157230 9662 54 123800 0.3 1 116115 7685 55 151573 0.3 1 142303 9270 56 178039 0.3 1 168271 9768 57 131467 0.3 1 122895 8572 58 147115 0.3 1 139737 7378 59 118925 0.3 1 111394 7531 60 151799 0.3 1 142575 9224 61 144120 0.3 1 136068 8052 62 147428 0.3 1 139233 8195 63 128075 0.3 1 119968 8107 64 135764 0.3 1 128209 7555 65 146614 0.3 1 138085 8529 66 155870 0.3 1 146365 9505 67 168571 0.3 1 156591 11980 68 310336 0.3 1 295745 14591 69 61543 0.3 1 56640 4903 70 21841 0.3 1 18433 3408 71 77515 0.3 1 72834 4681 72 115950 0.3 1 109389 6561 73 122667 0.3 1 115604 7063 74 120840 0.3 1 113936 6904 75 118343 0.3 1 111514 6829 76 117750 0.3 1 110989 6761 77 117217 0.3 1 110486 6731 78 109143 0.3 1 102786 6357 79 107883 0.3 1 101668 6215 80 105101 0.3 1 99015 6086 81 104048 0.3 1 98069 5979 82 100791 0.3 1 95040 5751 83 96002 0.3 1 90436 5566 84 92813 0.3 1 87473 5340 85 89718 0.3 1 84646 5072 86 86520 0.3 1 81561 4959 87 81906 0.3 1 77243 4663 88 81347 0.3 1 76501 4846 89 76428 0.3 1 72015 4413 90 76790 0.3 1 72233 4557 91 72129 0.3 1 67780 4349 92 67716 0.3 1 63638 4078 93 63437 0.3 1 59587 3850 94 61274 0.3 1 57720 3554 95 56931 0.3 1 53504 3427 96 53326 0.3 1 50061 3265 97 50390 0.3 1 47429 2961 98 46074 0.3 1 43201 2873 99 45190 0.3 1 42231 2959 100 40830 0.3 1 38265 2565 101 37913 0.3 1 35541 2372 102 35110 0.3 1 32897 2213 103 31900 0.3 1 29985 1915 104 30069 0.3 1 28092 1977 105 26590 0.3 1 24861 1729 106 23847 0.3 1 22283 1564 107 21922 0.3 1 20517 1405 108 20575 0.3 1 19261 1314 109 18220 0.3 1 17014 1206 110 16359 0.3 1 15225 1134 111 14698 0.3 1 13709 989 112 12826 0.3 1 11919 907 113 11006 0.3 1 10256 750 114 9719 0.3 1 9039 680 115 8407 0.3 1 7839 568 116 7289 0.3 1 6725 564 117 6390 0.3 1 5903 487 118 5317 0.3 1 4911 406 119 4366 0.3 1 4006 360 120 3632 0.3 1 3354 278 121 3334 0.3 1 3055 279 122 2775 0.3 1 2532 243 123 2262 0.3 1 2067 195 124 1853 0.3 1 1718 135 125 1573 0.3 1 1418 155 126 1249 0.3 1 1114 135 127 1068 0.3 1 970 98 128 811 0.3 1 720 91 129 753 0.3 1 679 74 130 521 0.3 1 476 45 131 504 0.3 1 454 50 132 357 0.3 1 326 31 133 348 0.3 1 306 42 134 413 0.3 1 388 25 135 242 0.3 1 222 20 136 135 0.3 1 122 13 137 135 0.3 1 121 14 138 66 0.3 1 62 4 139 41 0.3 1 36 5 140 32 0.3 1 27 5 141 40 0.3 1 34 6 142 26 0.3 1 24 2 143 30 0.3 1 25 5 144 18 0.3 1 15 3 145 14 0.3 1 12 2 146 21 0.3 1 19 2 147 69 0.3 1 65 4 148 44 0.3 1 40 4 149 37 0.3 1 35 2 150 304 0.3 1 264 40 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_L001_R1_001.fastq.gz ============================================= 18576202 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2936 (0.0%)