SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_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_2_S14_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 723.87 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 17,243,447 Reads with adapters: 13,329,210 (77.3%) Reads written (passing filters): 17,243,447 (100.0%) Total basepairs processed: 2,586,517,050 bp Quality-trimmed: 5,286,503 bp (0.2%) Total written (filtered): 2,048,045,774 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13329210 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.2% G: 20.5% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2371278 4310861.8 0 2371278 2 355428 1077715.4 0 355428 3 196735 269428.9 0 196735 4 114807 67357.2 0 114807 5 92976 16839.3 0 92976 6 90363 4209.8 0 90363 7 74432 1052.5 0 74432 8 93807 263.1 0 93807 9 93533 65.8 0 92435 1098 10 87230 16.4 1 82587 4643 11 96624 4.1 1 89271 7353 12 92957 1.0 1 86987 5970 13 93747 0.3 1 87764 5983 14 96011 0.3 1 89197 6814 15 98978 0.3 1 92592 6386 16 98159 0.3 1 90785 7374 17 119944 0.3 1 110196 9748 18 100650 0.3 1 94699 5951 19 86734 0.3 1 81180 5554 20 104244 0.3 1 97548 6696 21 115327 0.3 1 107159 8168 22 97273 0.3 1 91575 5698 23 115900 0.3 1 108235 7665 24 104136 0.3 1 95675 8461 25 112997 0.3 1 105393 7604 26 102184 0.3 1 96084 6100 27 114471 0.3 1 106298 8173 28 113184 0.3 1 105296 7888 29 118291 0.3 1 108737 9554 30 125680 0.3 1 118630 7050 31 99517 0.3 1 93132 6385 32 120246 0.3 1 112659 7587 33 112299 0.3 1 104687 7612 34 122051 0.3 1 114065 7986 35 122132 0.3 1 112527 9605 36 121056 0.3 1 113558 7498 37 131245 0.3 1 122809 8436 38 117529 0.3 1 109870 7659 39 130463 0.3 1 121802 8661 40 125603 0.3 1 117585 8018 41 145134 0.3 1 134544 10590 42 108964 0.3 1 101116 7848 43 193675 0.3 1 183736 9939 44 56524 0.3 1 51515 5009 45 130295 0.3 1 122170 8125 46 121941 0.3 1 114229 7712 47 128745 0.3 1 120966 7779 48 126992 0.3 1 118817 8175 49 138745 0.3 1 128994 9751 50 118346 0.3 1 111437 6909 51 127998 0.3 1 119617 8381 52 132118 0.3 1 122819 9299 53 142995 0.3 1 134373 8622 54 111526 0.3 1 104331 7195 55 132598 0.3 1 124212 8386 56 162335 0.3 1 152964 9371 57 103809 0.3 1 96508 7301 58 132526 0.3 1 125372 7154 59 115914 0.3 1 108457 7457 60 128350 0.3 1 120205 8145 61 126189 0.3 1 118700 7489 62 137584 0.3 1 129699 7885 63 110035 0.3 1 102791 7244 64 120964 0.3 1 114082 6882 65 135744 0.3 1 127467 8277 66 140396 0.3 1 131867 8529 67 145532 0.3 1 134835 10697 68 287021 0.3 1 273202 13819 69 48096 0.3 1 43999 4097 70 18303 0.3 1 15162 3141 71 72881 0.3 1 68623 4258 72 103446 0.3 1 97521 5925 73 109833 0.3 1 103450 6383 74 107925 0.3 1 101499 6426 75 106292 0.3 1 100152 6140 76 104330 0.3 1 98203 6127 77 104241 0.3 1 98017 6224 78 98088 0.3 1 92293 5795 79 96948 0.3 1 91096 5852 80 94252 0.3 1 88790 5462 81 93362 0.3 1 87783 5579 82 90202 0.3 1 84811 5391 83 87147 0.3 1 81902 5245 84 83793 0.3 1 78976 4817 85 80030 0.3 1 75251 4779 86 77694 0.3 1 73076 4618 87 74005 0.3 1 69629 4376 88 72748 0.3 1 68492 4256 89 68708 0.3 1 64648 4060 90 68047 0.3 1 63799 4248 91 64435 0.3 1 60450 3985 92 60503 0.3 1 56736 3767 93 56921 0.3 1 53460 3461 94 55199 0.3 1 51895 3304 95 50827 0.3 1 47651 3176 96 48189 0.3 1 45189 3000 97 45155 0.3 1 42374 2781 98 41036 0.3 1 38566 2470 99 40350 0.3 1 37693 2657 100 35870 0.3 1 33662 2208 101 33328 0.3 1 31103 2225 102 30823 0.3 1 28817 2006 103 28586 0.3 1 26749 1837 104 26108 0.3 1 24403 1705 105 23329 0.3 1 21857 1472 106 21254 0.3 1 19878 1376 107 19359 0.3 1 18082 1277 108 18005 0.3 1 16770 1235 109 16024 0.3 1 14870 1154 110 14310 0.3 1 13331 979 111 12919 0.3 1 11980 939 112 11039 0.3 1 10251 788 113 9662 0.3 1 8961 701 114 8278 0.3 1 7631 647 115 7400 0.3 1 6862 538 116 6380 0.3 1 5871 509 117 5590 0.3 1 5116 474 118 4883 0.3 1 4498 385 119 3958 0.3 1 3624 334 120 3465 0.3 1 3177 288 121 3026 0.3 1 2769 257 122 2531 0.3 1 2300 231 123 2116 0.3 1 1896 220 124 1699 0.3 1 1542 157 125 1434 0.3 1 1302 132 126 1188 0.3 1 1073 115 127 1126 0.3 1 995 131 128 869 0.3 1 759 110 129 701 0.3 1 622 79 130 549 0.3 1 500 49 131 448 0.3 1 398 50 132 432 0.3 1 385 47 133 454 0.3 1 410 44 134 600 0.3 1 564 36 135 275 0.3 1 252 23 136 173 0.3 1 157 16 137 109 0.3 1 101 8 138 92 0.3 1 82 10 139 63 0.3 1 54 9 140 64 0.3 1 52 12 141 59 0.3 1 51 8 142 40 0.3 1 37 3 143 53 0.3 1 48 5 144 32 0.3 1 31 1 145 53 0.3 1 50 3 146 166 0.3 1 154 12 147 548 0.3 1 525 23 148 402 0.3 1 390 12 149 263 0.3 1 250 13 150 2873 0.3 1 2693 180 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_L001_R1_001.fastq.gz ============================================= 17243447 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7271 (0.0%)