SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_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/8C_32psu_1_S5_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 508.63 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 13,980,098 Reads with adapters: 12,441,322 (89.0%) Reads written (passing filters): 13,980,098 (100.0%) Total basepairs processed: 2,097,014,700 bp Quality-trimmed: 11,100,984 bp (0.5%) Total written (filtered): 1,388,068,565 bp (66.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12441322 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.9% C: 13.5% G: 25.9% T: 33.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 845065 3495024.5 0 845065 2 141219 873756.1 0 141219 3 93432 218439.0 0 93432 4 54397 54609.8 0 54397 5 54738 13652.4 0 54738 6 49515 3413.1 0 49515 7 40356 853.3 0 40356 8 58207 213.3 0 58207 9 46723 53.3 0 46571 152 10 50819 13.3 1 47536 3283 11 55858 3.3 1 51611 4247 12 55535 0.8 1 51267 4268 13 64627 0.2 1 59860 4767 14 60188 0.2 1 55222 4966 15 49387 0.2 1 45866 3521 16 72997 0.2 1 67649 5348 17 62490 0.2 1 57882 4608 18 55351 0.2 1 51495 3856 19 73045 0.2 1 67571 5474 20 69542 0.2 1 64858 4684 21 61947 0.2 1 57754 4193 22 70571 0.2 1 65755 4816 23 75040 0.2 1 69830 5210 24 75107 0.2 1 69631 5476 25 86702 0.2 1 81241 5461 26 72229 0.2 1 66945 5284 27 82253 0.2 1 76106 6147 28 73797 0.2 1 69537 4260 29 84769 0.2 1 79179 5590 30 80847 0.2 1 75988 4859 31 93818 0.2 1 87884 5934 32 80840 0.2 1 75981 4859 33 94296 0.2 1 88030 6266 34 125592 0.2 1 117608 7984 35 67216 0.2 1 63145 4071 36 97900 0.2 1 91347 6553 37 105322 0.2 1 98633 6689 38 99129 0.2 1 93524 5605 39 95232 0.2 1 90264 4968 40 111486 0.2 1 104598 6888 41 108655 0.2 1 102291 6364 42 112712 0.2 1 106221 6491 43 103445 0.2 1 97749 5696 44 122874 0.2 1 115506 7368 45 132722 0.2 1 124931 7791 46 94746 0.2 1 89536 5210 47 122933 0.2 1 116693 6240 48 121112 0.2 1 114755 6357 49 129508 0.2 1 122295 7213 50 125201 0.2 1 118349 6852 51 157565 0.2 1 148874 8691 52 113806 0.2 1 107741 6065 53 143800 0.2 1 136726 7074 54 105294 0.2 1 100142 5152 55 140198 0.2 1 133598 6600 56 145988 0.2 1 138211 7777 57 140653 0.2 1 134358 6295 58 138055 0.2 1 131586 6469 59 139154 0.2 1 132424 6730 60 148619 0.2 1 141526 7093 61 153296 0.2 1 146146 7150 62 170542 0.2 1 162169 8373 63 228765 0.2 1 219044 9721 64 207127 0.2 1 199944 7183 65 126856 0.2 1 121054 5802 66 139494 0.2 1 133042 6452 67 139853 0.2 1 133076 6777 68 143593 0.2 1 136916 6677 69 142441 0.2 1 135436 7005 70 151914 0.2 1 144843 7071 71 164443 0.2 1 156971 7472 72 157523 0.2 1 150188 7335 73 168905 0.2 1 161158 7747 74 154929 0.2 1 147615 7314 75 149956 0.2 1 142906 7050 76 146942 0.2 1 140083 6859 77 148479 0.2 1 141471 7008 78 143688 0.2 1 136908 6780 79 140442 0.2 1 133903 6539 80 140871 0.2 1 134402 6469 81 139994 0.2 1 133731 6263 82 136315 0.2 1 130107 6208 83 133480 0.2 1 127541 5939 84 130953 0.2 1 125135 5818 85 130441 0.2 1 124710 5731 86 132446 0.2 1 126752 5694 87 133712 0.2 1 128137 5575 88 132133 0.2 1 126501 5632 89 120737 0.2 1 115669 5068 90 117385 0.2 1 112365 5020 91 111344 0.2 1 106559 4785 92 105918 0.2 1 101512 4406 93 103040 0.2 1 98784 4256 94 100992 0.2 1 96771 4221 95 96578 0.2 1 92479 4099 96 93826 0.2 1 89971 3855 97 86326 0.2 1 82928 3398 98 81391 0.2 1 78062 3329 99 79676 0.2 1 76340 3336 100 71969 0.2 1 68956 3013 101 69033 0.2 1 66191 2842 102 66979 0.2 1 64266 2713 103 62488 0.2 1 59972 2516 104 59740 0.2 1 57324 2416 105 53204 0.2 1 51066 2138 106 49286 0.2 1 47321 1965 107 44161 0.2 1 42327 1834 108 41055 0.2 1 39500 1555 109 37107 0.2 1 35641 1466 110 34404 0.2 1 32996 1408 111 32112 0.2 1 30868 1244 112 28362 0.2 1 27169 1193 113 24976 0.2 1 23918 1058 114 22140 0.2 1 21281 859 115 18628 0.2 1 17866 762 116 16277 0.2 1 15608 669 117 13249 0.2 1 12647 602 118 12071 0.2 1 11527 544 119 10131 0.2 1 9673 458 120 8604 0.2 1 8215 389 121 7264 0.2 1 6947 317 122 6137 0.2 1 5844 293 123 5194 0.2 1 4979 215 124 4472 0.2 1 4261 211 125 3689 0.2 1 3519 170 126 3057 0.2 1 2936 121 127 2513 0.2 1 2380 133 128 1994 0.2 1 1883 111 129 1536 0.2 1 1459 77 130 1296 0.2 1 1243 53 131 1130 0.2 1 1079 51 132 980 0.2 1 938 42 133 1174 0.2 1 1133 41 134 1195 0.2 1 1157 38 135 568 0.2 1 538 30 136 352 0.2 1 335 17 137 213 0.2 1 202 11 138 143 0.2 1 132 11 139 111 0.2 1 103 8 140 71 0.2 1 64 7 141 52 0.2 1 46 6 142 65 0.2 1 60 5 143 34 0.2 1 32 2 144 27 0.2 1 25 2 145 36 0.2 1 30 6 146 27 0.2 1 25 2 147 78 0.2 1 72 6 148 68 0.2 1 62 6 149 57 0.2 1 55 2 150 443 0.2 1 415 28 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_L002_R2_001.fastq.gz ============================================= 13980098 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 20569 (0.1%)