SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L002_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_32psu_2_S2_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 682.27 s (39 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 17,682,252 Reads with adapters: 14,725,601 (83.3%) Reads written (passing filters): 17,682,252 (100.0%) Total basepairs processed: 2,652,337,800 bp Quality-trimmed: 5,252,718 bp (0.2%) Total written (filtered): 1,953,712,678 bp (73.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14725601 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 12.9% G: 21.9% T: 35.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1730837 4420563.0 0 1730837 2 274288 1105140.8 0 274288 3 164540 276285.2 0 164540 4 98245 69071.3 0 98245 5 85133 17267.8 0 85133 6 82977 4317.0 0 82977 7 68628 1079.2 0 68628 8 92219 269.8 0 92219 9 82148 67.5 0 81058 1090 10 81207 16.9 1 75933 5274 11 91764 4.2 1 83517 8247 12 88451 1.1 1 81680 6771 13 90852 0.3 1 83635 7217 14 92006 0.3 1 84006 8000 15 95802 0.3 1 88019 7783 16 94793 0.3 1 86152 8641 17 117965 0.3 1 106745 11220 18 99003 0.3 1 91800 7203 19 85234 0.3 1 78539 6695 20 103603 0.3 1 95615 7988 21 115441 0.3 1 106021 9420 22 96644 0.3 1 89824 6820 23 112899 0.3 1 103928 8971 24 106903 0.3 1 96909 9994 25 114269 0.3 1 105193 9076 26 105406 0.3 1 97809 7597 27 119549 0.3 1 109420 10129 28 117559 0.3 1 108344 9215 29 126569 0.3 1 115202 11367 30 135359 0.3 1 126047 9312 31 102444 0.3 1 94598 7846 32 135060 0.3 1 124361 10699 33 113717 0.3 1 104773 8944 34 130221 0.3 1 118947 11274 35 139590 0.3 1 127417 12173 36 127748 0.3 1 118449 9299 37 156612 0.3 1 144323 12289 38 124619 0.3 1 114023 10596 39 136370 0.3 1 126274 10096 40 143456 0.3 1 132041 11415 41 145337 0.3 1 132898 12439 42 139531 0.3 1 126917 12614 43 211559 0.3 1 197954 13605 44 73750 0.3 1 66328 7422 45 151399 0.3 1 140473 10926 46 138024 0.3 1 127568 10456 47 150595 0.3 1 139553 11042 48 147780 0.3 1 136652 11128 49 162871 0.3 1 149899 12972 50 141270 0.3 1 131458 9812 51 154346 0.3 1 142859 11487 52 160748 0.3 1 148256 12492 53 167551 0.3 1 155619 11932 54 139669 0.3 1 129569 10100 55 162273 0.3 1 150174 12099 56 200304 0.3 1 186484 13820 57 127569 0.3 1 117186 10383 58 167466 0.3 1 156693 10773 59 150014 0.3 1 138880 11134 60 160710 0.3 1 148928 11782 61 158834 0.3 1 147715 11119 62 178143 0.3 1 165938 12205 63 141715 0.3 1 130934 10781 64 158746 0.3 1 148093 10653 65 176936 0.3 1 164216 12720 66 182618 0.3 1 169484 13134 67 198670 0.3 1 182225 16445 68 365118 0.3 1 345570 19548 69 68264 0.3 1 62074 6190 70 29092 0.3 1 24265 4827 71 103442 0.3 1 96474 6968 72 142212 0.3 1 133025 9187 73 149684 0.3 1 139925 9759 74 148896 0.3 1 138764 10132 75 148109 0.3 1 137782 10327 76 146530 0.3 1 136141 10389 77 146539 0.3 1 136490 10049 78 139703 0.3 1 129860 9843 79 137432 0.3 1 127635 9797 80 135397 0.3 1 125660 9737 81 133287 0.3 1 123761 9526 82 129169 0.3 1 119849 9320 83 125954 0.3 1 117089 8865 84 121677 0.3 1 112941 8736 85 117830 0.3 1 109511 8319 86 114988 0.3 1 106799 8189 87 110799 0.3 1 103288 7511 88 109823 0.3 1 102149 7674 89 103812 0.3 1 96531 7281 90 101371 0.3 1 94159 7212 91 96555 0.3 1 89763 6792 92 92588 0.3 1 86028 6560 93 86787 0.3 1 80806 5981 94 84568 0.3 1 78482 6086 95 78600 0.3 1 72903 5697 96 74361 0.3 1 69003 5358 97 69748 0.3 1 64791 4957 98 65245 0.3 1 60478 4767 99 62580 0.3 1 57800 4780 100 56847 0.3 1 52715 4132 101 53263 0.3 1 49277 3986 102 48648 0.3 1 45084 3564 103 45338 0.3 1 42014 3324 104 41917 0.3 1 38870 3047 105 37301 0.3 1 34586 2715 106 33679 0.3 1 31071 2608 107 30205 0.3 1 27947 2258 108 27998 0.3 1 25811 2187 109 24717 0.3 1 22799 1918 110 22343 0.3 1 20572 1771 111 20279 0.3 1 18723 1556 112 17492 0.3 1 16037 1455 113 14993 0.3 1 13741 1252 114 13102 0.3 1 12018 1084 115 11167 0.3 1 10176 991 116 9702 0.3 1 8851 851 117 8008 0.3 1 7282 726 118 6784 0.3 1 6194 590 119 5714 0.3 1 5190 524 120 4836 0.3 1 4363 473 121 3994 0.3 1 3606 388 122 3193 0.3 1 2889 304 123 2794 0.3 1 2493 301 124 2161 0.3 1 1934 227 125 1832 0.3 1 1606 226 126 1531 0.3 1 1356 175 127 1197 0.3 1 1054 143 128 960 0.3 1 854 106 129 853 0.3 1 753 100 130 591 0.3 1 514 77 131 531 0.3 1 470 61 132 430 0.3 1 380 50 133 462 0.3 1 411 51 134 470 0.3 1 418 52 135 263 0.3 1 225 38 136 146 0.3 1 127 19 137 106 0.3 1 90 16 138 84 0.3 1 66 18 139 59 0.3 1 48 11 140 48 0.3 1 41 7 141 28 0.3 1 20 8 142 22 0.3 1 17 5 143 22 0.3 1 15 7 144 21 0.3 1 19 2 145 41 0.3 1 38 3 146 29 0.3 1 26 3 147 81 0.3 1 70 11 148 47 0.3 1 39 8 149 50 0.3 1 42 8 150 504 0.3 1 392 112 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L002_R1_001.fastq.gz ============================================= 17682252 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3479 (0.0%)