SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_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/16C_26psu_1_S13_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 979.66 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 22,159,935 Reads with adapters: 17,263,070 (77.9%) Reads written (passing filters): 22,159,935 (100.0%) Total basepairs processed: 3,323,990,250 bp Quality-trimmed: 16,760,179 bp (0.5%) Total written (filtered): 2,603,569,143 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17263070 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.4% G: 23.7% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2980698 5539983.8 0 2980698 2 434290 1384995.9 0 434290 3 244115 346249.0 0 244115 4 143736 86562.2 0 143736 5 130207 21640.6 0 130207 6 112454 5410.1 0 112454 7 91383 1352.5 0 91383 8 130413 338.1 0 130413 9 102897 84.5 0 102495 402 10 113241 21.1 1 107719 5522 11 119188 5.3 1 111572 7616 12 120663 1.3 1 112735 7928 13 133942 0.3 1 125965 7977 14 126547 0.3 1 117452 9095 15 102830 0.3 1 96138 6692 16 149163 0.3 1 139761 9402 17 119889 0.3 1 111631 8258 18 113552 0.3 1 106594 6958 19 144826 0.3 1 135202 9624 20 135016 0.3 1 126722 8294 21 118040 0.3 1 110327 7713 22 135122 0.3 1 126795 8327 23 139623 0.3 1 130868 8755 24 139327 0.3 1 130312 9015 25 156486 0.3 1 147346 9140 26 131367 0.3 1 122873 8494 27 144343 0.3 1 134126 10217 28 135732 0.3 1 128445 7287 29 144460 0.3 1 135341 9119 30 143460 0.3 1 135475 7985 31 154935 0.3 1 145507 9428 32 140211 0.3 1 132501 7710 33 154714 0.3 1 145023 9691 34 197197 0.3 1 185506 11691 35 114069 0.3 1 107701 6368 36 154713 0.3 1 145095 9618 37 166945 0.3 1 157027 9918 38 155394 0.3 1 147358 8036 39 151879 0.3 1 143914 7965 40 168764 0.3 1 158797 9967 41 162964 0.3 1 154146 8818 42 166211 0.3 1 157158 9053 43 152395 0.3 1 144005 8390 44 174656 0.3 1 164812 9844 45 186871 0.3 1 176811 10060 46 135036 0.3 1 127666 7370 47 168636 0.3 1 159853 8783 48 166288 0.3 1 157802 8486 49 174530 0.3 1 165351 9179 50 164769 0.3 1 155907 8862 51 207765 0.3 1 197011 10754 52 147151 0.3 1 139795 7356 53 177051 0.3 1 168817 8234 54 133625 0.3 1 126900 6725 55 174567 0.3 1 166338 8229 56 178950 0.3 1 169886 9064 57 168945 0.3 1 161037 7908 58 161931 0.3 1 154618 7313 59 165789 0.3 1 157874 7915 60 171736 0.3 1 163328 8408 61 175826 0.3 1 167046 8780 62 192123 0.3 1 182534 9589 63 252743 0.3 1 241513 11230 64 207112 0.3 1 199124 7988 65 135660 0.3 1 129354 6306 66 145866 0.3 1 139110 6756 67 145748 0.3 1 138731 7017 68 146161 0.3 1 139522 6639 69 144487 0.3 1 137768 6719 70 154292 0.3 1 147160 7132 71 158353 0.3 1 151327 7026 72 150227 0.3 1 143181 7046 73 157376 0.3 1 150704 6672 74 144388 0.3 1 138042 6346 75 137234 0.3 1 131094 6140 76 133825 0.3 1 127901 5924 77 133664 0.3 1 127640 6024 78 127632 0.3 1 121889 5743 79 122934 0.3 1 117397 5537 80 122791 0.3 1 117317 5474 81 119094 0.3 1 113976 5118 82 115048 0.3 1 109953 5095 83 110957 0.3 1 106119 4838 84 107760 0.3 1 102959 4801 85 105919 0.3 1 100973 4946 86 104575 0.3 1 99936 4639 87 105119 0.3 1 100537 4582 88 102473 0.3 1 97892 4581 89 90861 0.3 1 86820 4041 90 87725 0.3 1 83791 3934 91 82796 0.3 1 79052 3744 92 76768 0.3 1 73386 3382 93 74497 0.3 1 71224 3273 94 71670 0.3 1 68502 3168 95 67300 0.3 1 64357 2943 96 63751 0.3 1 61088 2663 97 58781 0.3 1 56250 2531 98 54871 0.3 1 52462 2409 99 53000 0.3 1 50773 2227 100 48407 0.3 1 46381 2026 101 45093 0.3 1 43177 1916 102 40752 0.3 1 38996 1756 103 37584 0.3 1 35906 1678 104 35749 0.3 1 34226 1523 105 31850 0.3 1 30464 1386 106 29282 0.3 1 28064 1218 107 26084 0.3 1 24956 1128 108 23726 0.3 1 22669 1057 109 21646 0.3 1 20704 942 110 19323 0.3 1 18515 808 111 18235 0.3 1 17436 799 112 15797 0.3 1 15095 702 113 13713 0.3 1 13089 624 114 11968 0.3 1 11416 552 115 10124 0.3 1 9656 468 116 8777 0.3 1 8354 423 117 7339 0.3 1 6995 344 118 6452 0.3 1 6137 315 119 5422 0.3 1 5101 321 120 4499 0.3 1 4281 218 121 3883 0.3 1 3680 203 122 3313 0.3 1 3156 157 123 2807 0.3 1 2669 138 124 2400 0.3 1 2285 115 125 2022 0.3 1 1907 115 126 1650 0.3 1 1555 95 127 1434 0.3 1 1346 88 128 1129 0.3 1 1055 74 129 969 0.3 1 902 67 130 682 0.3 1 644 38 131 587 0.3 1 552 35 132 523 0.3 1 500 23 133 524 0.3 1 494 30 134 633 0.3 1 604 29 135 337 0.3 1 318 19 136 197 0.3 1 186 11 137 147 0.3 1 133 14 138 92 0.3 1 88 4 139 79 0.3 1 71 8 140 57 0.3 1 52 5 141 37 0.3 1 35 2 142 37 0.3 1 35 2 143 25 0.3 1 20 5 144 20 0.3 1 20 145 26 0.3 1 25 1 146 24 0.3 1 23 1 147 85 0.3 1 85 148 61 0.3 1 59 2 149 39 0.3 1 36 3 150 325 0.3 1 310 15 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L001_R2_001.fastq.gz ============================================= 22159935 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 29940 (0.1%)