SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_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_1_S13_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 921.66 s (42 us/read; 1.44 M reads/minute). === Summary === Total reads processed: 22,159,935 Reads with adapters: 17,366,785 (78.4%) Reads written (passing filters): 22,159,935 (100.0%) Total basepairs processed: 3,323,990,250 bp Quality-trimmed: 20,636,466 bp (0.6%) Total written (filtered): 2,599,584,885 bp (78.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17366785 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.0% G: 20.5% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2904827 5539983.8 0 2904827 2 423079 1384995.9 0 423079 3 231866 346249.0 0 231866 4 143449 86562.2 0 143449 5 117570 21640.6 0 117570 6 115529 5410.1 0 115529 7 96119 1352.5 0 96119 8 119364 338.1 0 119364 9 118406 84.5 0 116886 1520 10 112051 21.1 1 106032 6019 11 122987 5.3 1 113734 9253 12 119477 1.3 1 111842 7635 13 120023 0.3 1 112246 7777 14 122963 0.3 1 114085 8878 15 127528 0.3 1 119209 8319 16 126445 0.3 1 117002 9443 17 152761 0.3 1 140488 12273 18 129037 0.3 1 121213 7824 19 112889 0.3 1 105773 7116 20 133616 0.3 1 125004 8612 21 146516 0.3 1 136291 10225 22 126419 0.3 1 119045 7374 23 145391 0.3 1 135716 9675 24 136894 0.3 1 125670 11224 25 145117 0.3 1 135313 9804 26 134897 0.3 1 126717 8180 27 148757 0.3 1 137734 11023 28 145635 0.3 1 135492 10143 29 153188 0.3 1 140948 12240 30 163373 0.3 1 154030 9343 31 130689 0.3 1 122129 8560 32 157390 0.3 1 147156 10234 33 145226 0.3 1 135269 9957 34 158524 0.3 1 147826 10698 35 161582 0.3 1 148734 12848 36 173098 0.3 1 162838 10260 37 141921 0.3 1 133053 8868 38 164933 0.3 1 154468 10465 39 167185 0.3 1 155913 11272 40 175799 0.3 1 163207 12592 41 197239 0.3 1 176427 20812 42 165247 0.3 1 150517 14730 43 270149 0.3 1 254538 15611 44 85600 0.3 1 76961 8639 45 197628 0.3 1 175697 21931 46 723044 0.3 1 688287 34757 47 254889 0.3 1 240372 14517 48 114855 0.3 1 101708 13147 49 409546 0.3 1 390013 19533 50 125438 0.3 1 116192 9246 51 110069 0.3 1 99667 10402 52 381945 0.3 1 364475 17470 53 196688 0.3 1 188239 8449 54 63003 0.3 1 58174 4829 55 106109 0.3 1 101117 4992 56 55521 0.3 1 50154 5367 57 169184 0.3 1 161794 7390 58 35182 0.3 1 32212 2970 59 44244 0.3 1 39185 5059 60 173147 0.3 1 165425 7722 61 86440 0.3 1 82402 4038 62 40559 0.3 1 36479 4080 63 130914 0.3 1 123404 7510 64 122315 0.3 1 116337 5978 65 65805 0.3 1 60428 5377 66 148115 0.3 1 139100 9015 67 175930 0.3 1 163369 12561 68 293688 0.3 1 278052 15636 69 189726 0.3 1 179114 10612 70 75474 0.3 1 69457 6017 71 27345 0.3 1 23952 3393 72 97969 0.3 1 91968 6001 73 138145 0.3 1 130111 8034 74 143624 0.3 1 135279 8345 75 142674 0.3 1 134066 8608 76 141682 0.3 1 133308 8374 77 141205 0.3 1 132947 8258 78 133036 0.3 1 124966 8070 79 131630 0.3 1 123633 7997 80 128859 0.3 1 121116 7743 81 126119 0.3 1 118667 7452 82 123492 0.3 1 116262 7230 83 118847 0.3 1 111615 7232 84 115583 0.3 1 108642 6941 85 111409 0.3 1 104817 6592 86 107099 0.3 1 100545 6554 87 102731 0.3 1 96477 6254 88 101527 0.3 1 95245 6282 89 95383 0.3 1 89600 5783 90 95037 0.3 1 89230 5807 91 89836 0.3 1 84395 5441 92 84977 0.3 1 79865 5112 93 79479 0.3 1 74762 4717 94 76672 0.3 1 72010 4662 95 70676 0.3 1 66313 4363 96 66886 0.3 1 62766 4120 97 63105 0.3 1 59150 3955 98 58813 0.3 1 55101 3712 99 56801 0.3 1 52921 3880 100 51251 0.3 1 47973 3278 101 48131 0.3 1 44969 3162 102 43975 0.3 1 41134 2841 103 40749 0.3 1 38132 2617 104 37602 0.3 1 35059 2543 105 33601 0.3 1 31318 2283 106 30687 0.3 1 28622 2065 107 27550 0.3 1 25698 1852 108 25919 0.3 1 24135 1784 109 23271 0.3 1 21584 1687 110 20524 0.3 1 19077 1447 111 18563 0.3 1 17263 1300 112 16204 0.3 1 15036 1168 113 14110 0.3 1 13017 1093 114 12321 0.3 1 11394 927 115 10629 0.3 1 9884 745 116 9483 0.3 1 8756 727 117 8057 0.3 1 7440 617 118 7067 0.3 1 6491 576 119 5777 0.3 1 5264 513 120 4917 0.3 1 4511 406 121 4181 0.3 1 3800 381 122 3506 0.3 1 3174 332 123 2912 0.3 1 2640 272 124 2546 0.3 1 2297 249 125 2101 0.3 1 1902 199 126 1717 0.3 1 1548 169 127 1536 0.3 1 1361 175 128 1201 0.3 1 1095 106 129 1012 0.3 1 912 100 130 739 0.3 1 668 71 131 638 0.3 1 572 66 132 553 0.3 1 500 53 133 556 0.3 1 500 56 134 665 0.3 1 607 58 135 362 0.3 1 324 38 136 207 0.3 1 176 31 137 143 0.3 1 128 15 138 99 0.3 1 86 13 139 84 0.3 1 72 12 140 58 0.3 1 50 8 141 42 0.3 1 38 4 142 37 0.3 1 29 8 143 24 0.3 1 22 2 144 25 0.3 1 17 8 145 26 0.3 1 22 4 146 29 0.3 1 21 8 147 85 0.3 1 77 8 148 64 0.3 1 59 5 149 40 0.3 1 35 5 150 355 0.3 1 318 37 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_1_S13_L001_R1_001.fastq.gz ============================================= 22159935 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 4155 (0.0%)