SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_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/16C_26psu_3_S15_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 608.39 s (41 us/read; 1.45 M reads/minute). === Summary === Total reads processed: 14,705,097 Reads with adapters: 11,084,660 (75.4%) Reads written (passing filters): 14,705,097 (100.0%) Total basepairs processed: 2,205,764,550 bp Quality-trimmed: 5,654,261 bp (0.3%) Total written (filtered): 1,768,343,252 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11084660 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 18.1% G: 19.4% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2274798 3676274.2 0 2274798 2 348366 919068.6 0 348366 3 204139 229767.1 0 204139 4 102009 57441.8 0 102009 5 74565 14360.4 0 74565 6 72782 3590.1 0 72782 7 57000 897.5 0 57000 8 74016 224.4 0 74016 9 74077 56.1 0 73070 1007 10 67767 14.0 1 63550 4217 11 78426 3.5 1 71779 6647 12 73178 0.9 1 67904 5274 13 73121 0.2 1 67865 5256 14 76375 0.2 1 70227 6148 15 78023 0.2 1 72295 5728 16 76757 0.2 1 70359 6398 17 96301 0.2 1 87532 8769 18 78109 0.2 1 72884 5225 19 66841 0.2 1 61960 4881 20 81976 0.2 1 75979 5997 21 91230 0.2 1 84192 7038 22 74923 0.2 1 70026 4897 23 89318 0.2 1 82578 6740 24 80595 0.2 1 73239 7356 25 88530 0.2 1 81693 6837 26 80024 0.2 1 74706 5318 27 90563 0.2 1 83032 7531 28 88117 0.2 1 81366 6751 29 90600 0.2 1 82528 8072 30 100870 0.2 1 94452 6418 31 72291 0.2 1 67161 5130 32 93105 0.2 1 86376 6729 33 85828 0.2 1 79302 6526 34 93973 0.2 1 87113 6860 35 95201 0.2 1 86703 8498 36 98814 0.2 1 91143 7671 37 92594 0.2 1 86632 5962 38 92492 0.2 1 85700 6792 39 99594 0.2 1 92552 7042 40 99241 0.2 1 91728 7513 41 109705 0.2 1 100318 9387 42 91534 0.2 1 84273 7261 43 144391 0.2 1 135954 8437 44 48359 0.2 1 43755 4604 45 101091 0.2 1 93630 7461 46 97319 0.2 1 90173 7146 47 102355 0.2 1 95522 6833 48 95140 0.2 1 87635 7505 49 109171 0.2 1 100789 8382 50 88275 0.2 1 82648 5627 51 96905 0.2 1 90014 6891 52 106355 0.2 1 97463 8892 53 116272 0.2 1 109052 7220 54 82504 0.2 1 76626 5878 55 104155 0.2 1 97146 7009 56 117878 0.2 1 110588 7290 57 94064 0.2 1 87248 6816 58 98547 0.2 1 93098 5449 59 78147 0.2 1 72464 5683 60 103609 0.2 1 96779 6830 61 99715 0.2 1 93367 6348 62 96712 0.2 1 90590 6122 63 91683 0.2 1 85401 6282 64 88404 0.2 1 82993 5411 65 98564 0.2 1 92125 6439 66 106366 0.2 1 99301 7065 67 113416 0.2 1 104214 9202 68 212253 0.2 1 201102 11151 69 52200 0.2 1 48055 4145 70 18616 0.2 1 15750 2866 71 46522 0.2 1 43178 3344 72 78090 0.2 1 73258 4832 73 85268 0.2 1 79938 5330 74 84510 0.2 1 79145 5365 75 84172 0.2 1 78812 5360 76 82514 0.2 1 77266 5248 77 82709 0.2 1 77348 5361 78 77578 0.2 1 72635 4943 79 76394 0.2 1 71265 5129 80 74740 0.2 1 69853 4887 81 73428 0.2 1 68638 4790 82 72487 0.2 1 67836 4651 83 69366 0.2 1 64850 4516 84 68485 0.2 1 64014 4471 85 65855 0.2 1 61694 4161 86 63892 0.2 1 59720 4172 87 59968 0.2 1 56023 3945 88 59481 0.2 1 55667 3814 89 57389 0.2 1 53698 3691 90 56546 0.2 1 52783 3763 91 53907 0.2 1 50295 3612 92 51001 0.2 1 47631 3370 93 48245 0.2 1 45064 3181 94 47040 0.2 1 43981 3059 95 44130 0.2 1 41149 2981 96 41844 0.2 1 38970 2874 97 39077 0.2 1 36479 2598 98 36411 0.2 1 33904 2507 99 35258 0.2 1 32713 2545 100 32027 0.2 1 29780 2247 101 30331 0.2 1 28259 2072 102 28208 0.2 1 26138 2070 103 26173 0.2 1 24325 1848 104 24471 0.2 1 22816 1655 105 21780 0.2 1 20187 1593 106 20446 0.2 1 18956 1490 107 18149 0.2 1 16771 1378 108 17180 0.2 1 15945 1235 109 15082 0.2 1 13906 1176 110 14103 0.2 1 12998 1105 111 13190 0.2 1 12191 999 112 11450 0.2 1 10565 885 113 9717 0.2 1 8858 859 114 8899 0.2 1 8160 739 115 7941 0.2 1 7316 625 116 6735 0.2 1 6226 509 117 5866 0.2 1 5379 487 118 5055 0.2 1 4584 471 119 4372 0.2 1 3977 395 120 3711 0.2 1 3362 349 121 3540 0.2 1 3243 297 122 2903 0.2 1 2643 260 123 2410 0.2 1 2172 238 124 2227 0.2 1 2020 207 125 1832 0.2 1 1640 192 126 1658 0.2 1 1492 166 127 1471 0.2 1 1327 144 128 1080 0.2 1 953 127 129 958 0.2 1 848 110 130 709 0.2 1 628 81 131 795 0.2 1 718 77 132 862 0.2 1 774 88 133 1124 0.2 1 1033 91 134 1984 0.2 1 1883 101 135 812 0.2 1 780 32 136 310 0.2 1 269 41 137 196 0.2 1 180 16 138 185 0.2 1 168 17 139 138 0.2 1 131 7 140 94 0.2 1 84 10 141 74 0.2 1 68 6 142 62 0.2 1 50 12 143 92 0.2 1 84 8 144 74 0.2 1 67 7 145 205 0.2 1 196 9 146 780 0.2 1 755 25 147 4835 0.2 1 4652 183 148 3283 0.2 1 3150 133 149 1826 0.2 1 1757 69 150 16714 0.2 1 15810 904 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_3_S15_L001_R1_001.fastq.gz ============================================= 14705097 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 34522 (0.2%)