SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L002_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/8C_32psu_3_S7_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 567.54 s (40 us/read; 1.49 M reads/minute). === Summary === Total reads processed: 14,120,008 Reads with adapters: 11,722,164 (83.0%) Reads written (passing filters): 14,120,008 (100.0%) Total basepairs processed: 2,118,001,200 bp Quality-trimmed: 10,398,441 bp (0.5%) Total written (filtered): 1,557,917,839 bp (73.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11722164 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.6% C: 13.3% G: 24.5% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1423484 3530002.0 0 1423484 2 217404 882500.5 0 217404 3 135747 220625.1 0 135747 4 77416 55156.3 0 77416 5 73163 13789.1 0 73163 6 65957 3447.3 0 65957 7 52727 861.8 0 52727 8 75617 215.5 0 75617 9 60824 53.9 0 60611 213 10 64613 13.5 1 60561 4052 11 71071 3.4 1 65663 5408 12 69904 0.8 1 64695 5209 13 80991 0.2 1 75018 5973 14 75627 0.2 1 69287 6340 15 61630 0.2 1 57275 4355 16 89541 0.2 1 82804 6737 17 75362 0.2 1 69553 5809 18 67936 0.2 1 63097 4839 19 88766 0.2 1 82324 6442 20 83180 0.2 1 77328 5852 21 74299 0.2 1 69124 5175 22 83499 0.2 1 77755 5744 23 88403 0.2 1 82296 6107 24 88389 0.2 1 82109 6280 25 100119 0.2 1 93881 6238 26 84031 0.2 1 77871 6160 27 93205 0.2 1 86091 7114 28 83882 0.2 1 78923 4959 29 95544 0.2 1 89031 6513 30 91423 0.2 1 85830 5593 31 102885 0.2 1 96159 6726 32 88346 0.2 1 83048 5298 33 103020 0.2 1 96084 6936 34 134691 0.2 1 125875 8816 35 71511 0.2 1 67043 4468 36 106372 0.2 1 99204 7168 37 111667 0.2 1 104414 7253 38 105292 0.2 1 99304 5988 39 99654 0.2 1 94273 5381 40 115518 0.2 1 108179 7339 41 111214 0.2 1 104737 6477 42 115443 0.2 1 108784 6659 43 104707 0.2 1 98628 6079 44 122428 0.2 1 115040 7388 45 129896 0.2 1 122003 7893 46 92988 0.2 1 87594 5394 47 119950 0.2 1 113634 6316 48 117307 0.2 1 110893 6414 49 123614 0.2 1 116211 7403 50 118595 0.2 1 111825 6770 51 146157 0.2 1 137800 8357 52 108528 0.2 1 102556 5972 53 133051 0.2 1 126144 6907 54 97258 0.2 1 92286 4972 55 128012 0.2 1 121714 6298 56 133239 0.2 1 125868 7371 57 126482 0.2 1 120493 5989 58 123495 0.2 1 117409 6086 59 123171 0.2 1 116902 6269 60 129991 0.2 1 123447 6544 61 132791 0.2 1 126344 6447 62 145203 0.2 1 137595 7608 63 193193 0.2 1 184570 8623 64 164505 0.2 1 158250 6255 65 106154 0.2 1 101191 4963 66 116219 0.2 1 110707 5512 67 115499 0.2 1 109857 5642 68 116592 0.2 1 111069 5523 69 115665 0.2 1 109783 5882 70 124608 0.2 1 118610 5998 71 128211 0.2 1 122084 6127 72 122112 0.2 1 116125 5987 73 126921 0.2 1 120760 6161 74 118790 0.2 1 112963 5827 75 113173 0.2 1 107712 5461 76 111463 0.2 1 105998 5465 77 111662 0.2 1 106140 5522 78 107207 0.2 1 101895 5312 79 104292 0.2 1 99234 5058 80 103845 0.2 1 98916 4929 81 101938 0.2 1 97104 4834 82 97773 0.2 1 93124 4649 83 95971 0.2 1 91487 4484 84 92983 0.2 1 88672 4311 85 91731 0.2 1 87597 4134 86 91538 0.2 1 87240 4298 87 90919 0.2 1 86818 4101 88 89775 0.2 1 85803 3972 89 80478 0.2 1 76988 3490 90 77967 0.2 1 74477 3490 91 73781 0.2 1 70569 3212 92 69447 0.2 1 66340 3107 93 66394 0.2 1 63362 3032 94 63823 0.2 1 61051 2772 95 60418 0.2 1 57617 2801 96 57934 0.2 1 55484 2450 97 54242 0.2 1 51870 2372 98 51153 0.2 1 49011 2142 99 50193 0.2 1 47988 2205 100 43401 0.2 1 41462 1939 101 41188 0.2 1 39459 1729 102 38238 0.2 1 36636 1602 103 35697 0.2 1 34094 1603 104 34260 0.2 1 32771 1489 105 30330 0.2 1 29031 1299 106 27539 0.2 1 26325 1214 107 24680 0.2 1 23635 1045 108 22009 0.2 1 21062 947 109 19974 0.2 1 19117 857 110 18015 0.2 1 17209 806 111 16915 0.2 1 16205 710 112 14332 0.2 1 13689 643 113 12446 0.2 1 11895 551 114 10968 0.2 1 10478 490 115 9016 0.2 1 8590 426 116 7818 0.2 1 7478 340 117 6323 0.2 1 6027 296 118 5766 0.2 1 5518 248 119 4704 0.2 1 4500 204 120 3901 0.2 1 3708 193 121 3388 0.2 1 3195 193 122 2862 0.2 1 2731 131 123 2458 0.2 1 2315 143 124 2060 0.2 1 1986 74 125 1642 0.2 1 1547 95 126 1477 0.2 1 1395 82 127 1193 0.2 1 1127 66 128 861 0.2 1 803 58 129 803 0.2 1 750 53 130 513 0.2 1 479 34 131 475 0.2 1 451 24 132 384 0.2 1 349 35 133 402 0.2 1 380 22 134 430 0.2 1 416 14 135 203 0.2 1 185 18 136 160 0.2 1 156 4 137 84 0.2 1 74 10 138 68 0.2 1 64 4 139 47 0.2 1 44 3 140 21 0.2 1 20 1 141 24 0.2 1 21 3 142 16 0.2 1 13 3 143 16 0.2 1 13 3 144 10 0.2 1 10 145 20 0.2 1 19 1 146 18 0.2 1 18 147 25 0.2 1 23 2 148 19 0.2 1 15 4 149 13 0.2 1 12 1 150 153 0.2 1 145 8 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_3_S7_L002_R2_001.fastq.gz ============================================= 14120008 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 16796 (0.1%)