SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_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/8C_32psu_3_S7_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 544.25 s (39 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 14,120,008 Reads with adapters: 11,800,625 (83.6%) Reads written (passing filters): 14,120,008 (100.0%) Total basepairs processed: 2,118,001,200 bp Quality-trimmed: 4,373,755 bp (0.2%) Total written (filtered): 1,553,898,462 bp (73.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11800625 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 15.1% G: 21.0% T: 34.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1368833 3530002.0 0 1368833 2 213297 882500.5 0 213297 3 129961 220625.1 0 129961 4 79035 55156.3 0 79035 5 69573 13789.1 0 69573 6 67663 3447.3 0 67663 7 54249 861.8 0 54249 8 69306 215.5 0 69306 9 69302 53.9 0 68512 790 10 64667 13.5 1 60704 3963 11 73696 3.4 1 67523 6173 12 69675 0.8 1 64547 5128 13 71952 0.2 1 66511 5441 14 73593 0.2 1 67472 6121 15 76996 0.2 1 70887 6109 16 75526 0.2 1 69104 6422 17 93355 0.2 1 84545 8810 18 79593 0.2 1 73933 5660 19 68124 0.2 1 63039 5085 20 82749 0.2 1 76505 6244 21 92275 0.2 1 85139 7136 22 77618 0.2 1 72438 5180 23 92025 0.2 1 84966 7059 24 85340 0.2 1 77863 7477 25 92374 0.2 1 85186 7188 26 84405 0.2 1 78632 5773 27 95395 0.2 1 87567 7828 28 93111 0.2 1 85941 7170 29 103004 0.2 1 93769 9235 30 106080 0.2 1 99144 6936 31 80431 0.2 1 74401 6030 32 102254 0.2 1 94262 7992 33 95806 0.2 1 88463 7343 34 106075 0.2 1 96928 9147 35 108269 0.2 1 99389 8880 36 112253 0.2 1 102783 9470 37 99044 0.2 1 92235 6809 38 121329 0.2 1 110516 10813 39 100947 0.2 1 93251 7696 40 114342 0.2 1 105610 8732 41 128592 0.2 1 117446 11146 42 100668 0.2 1 92131 8537 43 169999 0.2 1 159204 10795 44 56249 0.2 1 50770 5479 45 119775 0.2 1 111031 8744 46 112063 0.2 1 103816 8247 47 119122 0.2 1 110508 8614 48 118788 0.2 1 109597 9191 49 131198 0.2 1 120814 10384 50 109980 0.2 1 102619 7361 51 122763 0.2 1 113852 8911 52 127644 0.2 1 117521 10123 53 136952 0.2 1 127680 9272 54 107784 0.2 1 99974 7810 55 130694 0.2 1 121255 9439 56 158527 0.2 1 147787 10740 57 103844 0.2 1 95331 8513 58 132382 0.2 1 124247 8135 59 116544 0.2 1 107902 8642 60 129622 0.2 1 120349 9273 61 128569 0.2 1 119774 8795 62 140522 0.2 1 130790 9732 63 114632 0.2 1 105994 8638 64 124792 0.2 1 116366 8426 65 140416 0.2 1 130644 9772 66 145932 0.2 1 135671 10261 67 159891 0.2 1 146767 13124 68 288595 0.2 1 272910 15685 69 63057 0.2 1 57575 5482 70 26024 0.2 1 21992 4032 71 79266 0.2 1 73983 5283 72 112824 0.2 1 105728 7096 73 119835 0.2 1 111892 7943 74 119611 0.2 1 111533 8078 75 117923 0.2 1 109788 8135 76 117731 0.2 1 109296 8435 77 118271 0.2 1 109919 8352 78 111566 0.2 1 103610 7956 79 111519 0.2 1 103611 7908 80 109197 0.2 1 101453 7744 81 107570 0.2 1 99856 7714 82 104569 0.2 1 97118 7451 83 102383 0.2 1 95228 7155 84 99102 0.2 1 92021 7081 85 96000 0.2 1 89098 6902 86 93524 0.2 1 86838 6686 87 89373 0.2 1 83285 6088 88 88917 0.2 1 82644 6273 89 84001 0.2 1 77961 6040 90 83693 0.2 1 77869 5824 91 80101 0.2 1 74574 5527 92 76032 0.2 1 70730 5302 93 71132 0.2 1 66158 4974 94 68649 0.2 1 63740 4909 95 64070 0.2 1 59484 4586 96 60750 0.2 1 56444 4306 97 57341 0.2 1 53268 4073 98 53260 0.2 1 49347 3913 99 52636 0.2 1 48599 4037 100 46791 0.2 1 43393 3398 101 44342 0.2 1 41093 3249 102 40590 0.2 1 37587 3003 103 37417 0.2 1 34694 2723 104 34470 0.2 1 31943 2527 105 30930 0.2 1 28658 2272 106 28279 0.2 1 26119 2160 107 25736 0.2 1 23845 1891 108 23849 0.2 1 22042 1807 109 21192 0.2 1 19537 1655 110 19116 0.2 1 17675 1441 111 17231 0.2 1 15808 1423 112 14798 0.2 1 13558 1240 113 12618 0.2 1 11582 1036 114 11317 0.2 1 10327 990 115 9619 0.2 1 8804 815 116 8405 0.2 1 7688 717 117 7048 0.2 1 6428 620 118 6316 0.2 1 5766 550 119 5076 0.2 1 4600 476 120 4250 0.2 1 3802 448 121 3670 0.2 1 3303 367 122 3096 0.2 1 2757 339 123 2589 0.2 1 2312 277 124 2201 0.2 1 1979 222 125 1708 0.2 1 1510 198 126 1570 0.2 1 1383 187 127 1266 0.2 1 1112 154 128 926 0.2 1 821 105 129 844 0.2 1 748 96 130 568 0.2 1 488 80 131 507 0.2 1 451 56 132 422 0.2 1 368 54 133 416 0.2 1 358 58 134 449 0.2 1 401 48 135 219 0.2 1 188 31 136 167 0.2 1 147 20 137 91 0.2 1 79 12 138 80 0.2 1 64 16 139 47 0.2 1 42 5 140 27 0.2 1 21 6 141 27 0.2 1 23 4 142 18 0.2 1 10 8 143 22 0.2 1 11 11 144 14 0.2 1 10 4 145 18 0.2 1 16 2 146 18 0.2 1 14 4 147 32 0.2 1 28 4 148 19 0.2 1 17 2 149 14 0.2 1 10 4 150 202 0.2 1 177 25 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L002_R1_001.fastq.gz ============================================= 14120008 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2849 (0.0%)