SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L001_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/8C_32psu_3_S7_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 557.64 s (39 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 14,166,205 Reads with adapters: 11,771,953 (83.1%) Reads written (passing filters): 14,166,205 (100.0%) Total basepairs processed: 2,124,930,750 bp Quality-trimmed: 10,797,724 bp (0.5%) Total written (filtered): 1,563,454,753 bp (73.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11771953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.6% C: 13.3% G: 24.5% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1427757 3541551.2 0 1427757 2 222493 885387.8 0 222493 3 133332 221347.0 0 133332 4 79137 55336.7 0 79137 5 75786 13834.2 0 75786 6 65915 3458.5 0 65915 7 53576 864.6 0 53576 8 76744 216.2 0 76744 9 61976 54.0 0 61779 197 10 67080 13.5 1 64106 2974 11 71681 3.4 1 67501 4180 12 72222 0.8 1 68053 4169 13 80561 0.2 1 76346 4215 14 76520 0.2 1 71606 4914 15 62607 0.2 1 59130 3477 16 91383 0.2 1 86350 5033 17 72745 0.2 1 68212 4533 18 70883 0.2 1 67020 3863 19 89801 0.2 1 84529 5272 20 83841 0.2 1 79367 4474 21 75027 0.2 1 70918 4109 22 84425 0.2 1 79923 4502 23 88024 0.2 1 83097 4927 24 88855 0.2 1 83891 4964 25 101226 0.2 1 95974 5252 26 83308 0.2 1 78591 4717 27 92909 0.2 1 87066 5843 28 87156 0.2 1 83145 4011 29 93947 0.2 1 88848 5099 30 93821 0.2 1 89436 4385 31 101908 0.2 1 96520 5388 32 92154 0.2 1 87903 4251 33 101850 0.2 1 96541 5309 34 132968 0.2 1 125972 6996 35 75102 0.2 1 71554 3548 36 106526 0.2 1 100872 5654 37 112114 0.2 1 106255 5859 38 106187 0.2 1 101516 4671 39 103250 0.2 1 98795 4455 40 116350 0.2 1 110242 6108 41 111543 0.2 1 106565 4978 42 115913 0.2 1 110317 5596 43 105510 0.2 1 100613 4897 44 121504 0.2 1 115737 5767 45 131840 0.2 1 125697 6143 46 94875 0.2 1 90604 4271 47 121018 0.2 1 115877 5141 48 118842 0.2 1 113797 5045 49 124446 0.2 1 118832 5614 50 118268 0.2 1 112777 5491 51 147285 0.2 1 140570 6715 52 109448 0.2 1 105060 4388 53 130385 0.2 1 125319 5066 54 99487 0.2 1 95470 4017 55 129239 0.2 1 124277 4962 56 133599 0.2 1 127967 5632 57 126390 0.2 1 121587 4803 58 121811 0.2 1 117475 4336 59 124529 0.2 1 119540 4989 60 130401 0.2 1 125258 5143 61 134015 0.2 1 128535 5480 62 145629 0.2 1 139763 5866 63 197423 0.2 1 190204 7219 64 168240 0.2 1 162928 5312 65 106543 0.2 1 102625 3918 66 114942 0.2 1 110706 4236 67 114164 0.2 1 109736 4428 68 116350 0.2 1 112096 4254 69 114565 0.2 1 110115 4450 70 124406 0.2 1 119762 4644 71 128031 0.2 1 123514 4517 72 120687 0.2 1 116066 4621 73 126907 0.2 1 122307 4600 74 117912 0.2 1 113666 4246 75 113448 0.2 1 109343 4105 76 111278 0.2 1 107269 4009 77 112780 0.2 1 108679 4101 78 106864 0.2 1 102856 4008 79 103353 0.2 1 99664 3689 80 103266 0.2 1 99595 3671 81 101983 0.2 1 98265 3718 82 97716 0.2 1 94285 3431 83 95425 0.2 1 92073 3352 84 92931 0.2 1 89513 3418 85 92256 0.2 1 88832 3424 86 91168 0.2 1 87863 3305 87 91423 0.2 1 88169 3254 88 89550 0.2 1 86420 3130 89 80366 0.2 1 77566 2800 90 77351 0.2 1 74500 2851 91 72940 0.2 1 70306 2634 92 68488 0.2 1 66133 2355 93 65935 0.2 1 63542 2393 94 63561 0.2 1 61328 2233 95 59923 0.2 1 57811 2112 96 58074 0.2 1 56092 1982 97 54057 0.2 1 52194 1863 98 50980 0.2 1 49204 1776 99 50084 0.2 1 48441 1643 100 43642 0.2 1 42153 1489 101 40618 0.2 1 39288 1330 102 38299 0.2 1 37001 1298 103 34998 0.2 1 33809 1189 104 34454 0.2 1 33375 1079 105 29814 0.2 1 28817 997 106 27473 0.2 1 26595 878 107 24384 0.2 1 23578 806 108 22338 0.2 1 21561 777 109 19549 0.2 1 18854 695 110 18085 0.2 1 17505 580 111 16893 0.2 1 16326 567 112 14541 0.2 1 14060 481 113 12649 0.2 1 12207 442 114 11108 0.2 1 10661 447 115 9325 0.2 1 9006 319 116 7950 0.2 1 7620 330 117 6499 0.2 1 6272 227 118 5695 0.2 1 5463 232 119 4844 0.2 1 4637 207 120 4029 0.2 1 3868 161 121 3484 0.2 1 3355 129 122 2831 0.2 1 2700 131 123 2522 0.2 1 2436 86 124 2113 0.2 1 2005 108 125 1739 0.2 1 1651 88 126 1465 0.2 1 1407 58 127 1198 0.2 1 1145 53 128 931 0.2 1 888 43 129 754 0.2 1 713 41 130 539 0.2 1 514 25 131 443 0.2 1 421 22 132 375 0.2 1 351 24 133 401 0.2 1 386 15 134 477 0.2 1 456 21 135 242 0.2 1 234 8 136 136 0.2 1 132 4 137 103 0.2 1 99 4 138 81 0.2 1 73 8 139 54 0.2 1 51 3 140 37 0.2 1 32 5 141 20 0.2 1 19 1 142 21 0.2 1 20 1 143 18 0.2 1 16 2 144 17 0.2 1 16 1 145 18 0.2 1 16 2 146 15 0.2 1 14 1 147 32 0.2 1 29 3 148 19 0.2 1 17 2 149 11 0.2 1 10 1 150 176 0.2 1 165 11 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L001_R2_001.fastq.gz ============================================= 14166205 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 18363 (0.1%)