SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_L002_R2_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/16C_26psu_3_S15_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 637.92 s (44 us/read; 1.38 M reads/minute). === Summary === Total reads processed: 14,622,552 Reads with adapters: 10,913,941 (74.6%) Reads written (passing filters): 14,622,552 (100.0%) Total basepairs processed: 2,193,382,800 bp Quality-trimmed: 13,012,389 bp (0.6%) Total written (filtered): 1,758,102,450 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10913941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 14.2% G: 23.9% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2243893 3655638.0 0 2243893 2 361235 913909.5 0 361235 3 221045 228477.4 0 221045 4 102953 57119.3 0 102953 5 80629 14279.8 0 80629 6 70223 3570.0 0 70223 7 53470 892.5 0 53470 8 79479 223.1 0 79479 9 62911 55.8 0 62617 294 10 66925 13.9 1 61688 5237 11 73700 3.5 1 66819 6881 12 72572 0.9 1 65940 6632 13 82700 0.2 1 75488 7212 14 76573 0.2 1 68946 7627 15 61263 0.2 1 55865 5398 16 90146 0.2 1 82109 8037 17 74386 0.2 1 67549 6837 18 67318 0.2 1 61385 5933 19 87145 0.2 1 79499 7646 20 80434 0.2 1 73597 6837 21 71959 0.2 1 65758 6201 22 80520 0.2 1 73704 6816 23 83808 0.2 1 76805 7003 24 83121 0.2 1 75853 7268 25 94721 0.2 1 87319 7402 26 78397 0.2 1 71438 6959 27 87589 0.2 1 79828 7761 28 77436 0.2 1 71759 5677 29 88231 0.2 1 81047 7184 30 81944 0.2 1 75545 6399 31 92581 0.2 1 85292 7289 32 80085 0.2 1 74132 5953 33 91916 0.2 1 84460 7456 34 117300 0.2 1 108202 9098 35 62830 0.2 1 57836 4994 36 92603 0.2 1 85123 7480 37 97494 0.2 1 89682 7812 38 93013 0.2 1 86322 6691 39 86916 0.2 1 80841 6075 40 100050 0.2 1 92533 7517 41 96502 0.2 1 89613 6889 42 98694 0.2 1 91554 7140 43 88091 0.2 1 81948 6143 44 102146 0.2 1 94589 7557 45 106497 0.2 1 98693 7804 46 77918 0.2 1 72391 5527 47 98307 0.2 1 91760 6547 48 96325 0.2 1 89754 6571 49 100699 0.2 1 93521 7178 50 95936 0.2 1 89184 6752 51 117412 0.2 1 109335 8077 52 84318 0.2 1 78674 5644 53 103753 0.2 1 97370 6383 54 76703 0.2 1 71688 5015 55 100303 0.2 1 94078 6225 56 104185 0.2 1 97076 7109 57 98544 0.2 1 92645 5899 58 94450 0.2 1 88927 5523 59 94831 0.2 1 88887 5944 60 99091 0.2 1 92777 6314 61 100905 0.2 1 94656 6249 62 109121 0.2 1 102218 6903 63 142655 0.2 1 134487 8168 64 117121 0.2 1 111484 5637 65 77324 0.2 1 72904 4420 66 84925 0.2 1 79850 5075 67 82998 0.2 1 77768 5230 68 84356 0.2 1 79351 5005 69 83969 0.2 1 78702 5267 70 86991 0.2 1 81734 5257 71 92058 0.2 1 86658 5400 72 87408 0.2 1 82156 5252 73 92562 0.2 1 87094 5468 74 84507 0.2 1 79446 5061 75 80670 0.2 1 75777 4893 76 78563 0.2 1 73818 4745 77 77927 0.2 1 73312 4615 78 73796 0.2 1 69197 4599 79 71841 0.2 1 67592 4249 80 70609 0.2 1 66510 4099 81 69349 0.2 1 65453 3896 82 67523 0.2 1 63514 4009 83 64665 0.2 1 60869 3796 84 63972 0.2 1 60280 3692 85 62543 0.2 1 58851 3692 86 62248 0.2 1 58801 3447 87 61991 0.2 1 58664 3327 88 61620 0.2 1 58173 3447 89 55062 0.2 1 51949 3113 90 52411 0.2 1 49511 2900 91 49315 0.2 1 46549 2766 92 47010 0.2 1 44328 2682 93 44789 0.2 1 42339 2450 94 43445 0.2 1 41012 2433 95 40986 0.2 1 38680 2306 96 39258 0.2 1 37094 2164 97 36644 0.2 1 34643 2001 98 34564 0.2 1 32670 1894 99 32993 0.2 1 31157 1836 100 31055 0.2 1 29316 1739 101 27872 0.2 1 26391 1481 102 25485 0.2 1 24012 1473 103 24164 0.2 1 22767 1397 104 23318 0.2 1 22028 1290 105 20591 0.2 1 19438 1153 106 19078 0.2 1 17973 1105 107 17270 0.2 1 16333 937 108 15786 0.2 1 14877 909 109 14538 0.2 1 13717 821 110 13063 0.2 1 12333 730 111 12532 0.2 1 11819 713 112 10933 0.2 1 10317 616 113 9707 0.2 1 9177 530 114 8352 0.2 1 7861 491 115 7373 0.2 1 6927 446 116 6174 0.2 1 5812 362 117 5508 0.2 1 5151 357 118 4695 0.2 1 4387 308 119 4109 0.2 1 3838 271 120 3479 0.2 1 3278 201 121 3246 0.2 1 3039 207 122 2778 0.2 1 2609 169 123 2432 0.2 1 2288 144 124 2091 0.2 1 1964 127 125 1753 0.2 1 1626 127 126 1569 0.2 1 1461 108 127 1430 0.2 1 1321 109 128 1051 0.2 1 972 79 129 984 0.2 1 936 48 130 686 0.2 1 639 47 131 713 0.2 1 668 45 132 719 0.2 1 681 38 133 1234 0.2 1 1177 57 134 2006 0.2 1 1917 89 135 763 0.2 1 728 35 136 321 0.2 1 299 22 137 192 0.2 1 179 13 138 174 0.2 1 164 10 139 115 0.2 1 111 4 140 101 0.2 1 87 14 141 72 0.2 1 66 6 142 70 0.2 1 63 7 143 96 0.2 1 90 6 144 66 0.2 1 61 5 145 236 0.2 1 225 11 146 987 0.2 1 943 44 147 4949 0.2 1 4744 205 148 3207 0.2 1 3070 137 149 1976 0.2 1 1884 92 150 15929 0.2 1 15207 722 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_L002_R2_001.fastq.gz ============================================= 14622552 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 54056 (0.4%)