SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_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_4_S16_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 690.05 s (40 us/read; 1.50 M reads/minute). === Summary === Total reads processed: 17,274,454 Reads with adapters: 13,728,900 (79.5%) Reads written (passing filters): 17,274,454 (100.0%) Total basepairs processed: 2,591,168,100 bp Quality-trimmed: 5,179,651 bp (0.2%) Total written (filtered): 1,987,019,797 bp (76.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13728900 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 17.1% G: 19.6% T: 33.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2136043 4318613.5 0 2136043 2 318200 1079653.4 0 318200 3 181191 269913.3 0 181191 4 105391 67478.3 0 105391 5 86281 16869.6 0 86281 6 85402 4217.4 0 85402 7 69532 1054.3 0 69532 8 89673 263.6 0 89673 9 85385 65.9 0 84182 1203 10 81888 16.5 1 77249 4639 11 92800 4.1 1 85219 7581 12 87898 1.0 1 82011 5887 13 88385 0.3 1 82215 6170 14 91465 0.3 1 84417 7048 15 93851 0.3 1 87200 6651 16 93365 0.3 1 85770 7595 17 112928 0.3 1 103341 9587 18 97669 0.3 1 91300 6369 19 82484 0.3 1 76767 5717 20 99682 0.3 1 92884 6798 21 110868 0.3 1 102713 8155 22 94466 0.3 1 88707 5759 23 107932 0.3 1 100154 7778 24 103619 0.3 1 94765 8854 25 110068 0.3 1 102116 7952 26 100495 0.3 1 94095 6400 27 112487 0.3 1 103684 8803 28 109738 0.3 1 101919 7819 29 116657 0.3 1 106828 9829 30 126889 0.3 1 119461 7428 31 92971 0.3 1 86609 6362 32 117804 0.3 1 109725 8079 33 111542 0.3 1 103765 7777 34 119656 0.3 1 110996 8660 35 119627 0.3 1 110861 8766 36 135056 0.3 1 123455 11601 37 141108 0.3 1 132535 8573 38 98717 0.3 1 92159 6558 39 131001 0.3 1 121415 9586 40 131538 0.3 1 121991 9547 41 151149 0.3 1 140064 11085 42 103859 0.3 1 95703 8156 43 200319 0.3 1 189316 11003 44 53496 0.3 1 48400 5096 45 131702 0.3 1 122909 8793 46 127887 0.3 1 119378 8509 47 129236 0.3 1 120995 8241 48 131832 0.3 1 122637 9195 49 143882 0.3 1 133714 10168 50 119251 0.3 1 111807 7444 51 131353 0.3 1 122552 8801 52 136704 0.3 1 126618 10086 53 148364 0.3 1 138822 9542 54 114737 0.3 1 107428 7309 55 140460 0.3 1 130746 9714 56 175570 0.3 1 164830 10740 57 103575 0.3 1 95859 7716 58 143113 0.3 1 134869 8244 59 126187 0.3 1 117760 8427 60 135064 0.3 1 125919 9145 61 135372 0.3 1 126642 8730 62 149463 0.3 1 140362 9101 63 114425 0.3 1 106420 8005 64 130898 0.3 1 122796 8102 65 148784 0.3 1 139139 9645 66 153297 0.3 1 143445 9852 67 160682 0.3 1 147924 12758 68 313433 0.3 1 297800 15633 69 49296 0.3 1 44675 4621 70 20166 0.3 1 16553 3613 71 84125 0.3 1 78872 5253 72 115954 0.3 1 109117 6837 73 122861 0.3 1 115327 7534 74 121230 0.3 1 113900 7330 75 120996 0.3 1 113426 7570 76 120220 0.3 1 112755 7465 77 120174 0.3 1 112559 7615 78 113112 0.3 1 105946 7166 79 112516 0.3 1 105557 6959 80 110113 0.3 1 103237 6876 81 108721 0.3 1 102021 6700 82 106548 0.3 1 99970 6578 83 102870 0.3 1 96372 6498 84 99814 0.3 1 93650 6164 85 97423 0.3 1 91330 6093 86 93928 0.3 1 88109 5819 87 90540 0.3 1 84909 5631 88 88338 0.3 1 82703 5635 89 85264 0.3 1 79857 5407 90 84889 0.3 1 79581 5308 91 80908 0.3 1 75799 5109 92 77367 0.3 1 72491 4876 93 72198 0.3 1 67528 4670 94 71195 0.3 1 66820 4375 95 66612 0.3 1 62421 4191 96 62397 0.3 1 58348 4049 97 59079 0.3 1 55329 3750 98 55292 0.3 1 51774 3518 99 54334 0.3 1 50683 3651 100 49120 0.3 1 45957 3163 101 46590 0.3 1 43597 2993 102 43817 0.3 1 40930 2887 103 40178 0.3 1 37514 2664 104 37716 0.3 1 35273 2443 105 33568 0.3 1 31289 2279 106 31261 0.3 1 29161 2100 107 28961 0.3 1 27009 1952 108 26580 0.3 1 24746 1834 109 24178 0.3 1 22520 1658 110 22331 0.3 1 20687 1644 111 19845 0.3 1 18444 1401 112 17480 0.3 1 16231 1249 113 15260 0.3 1 14048 1212 114 13572 0.3 1 12544 1028 115 12245 0.3 1 11265 980 116 10672 0.3 1 9863 809 117 9108 0.3 1 8423 685 118 7910 0.3 1 7333 577 119 6724 0.3 1 6143 581 120 5760 0.3 1 5265 495 121 5240 0.3 1 4780 460 122 4324 0.3 1 3902 422 123 3607 0.3 1 3320 287 124 3039 0.3 1 2741 298 125 2579 0.3 1 2329 250 126 2117 0.3 1 1915 202 127 1827 0.3 1 1662 165 128 1426 0.3 1 1277 149 129 1179 0.3 1 1062 117 130 902 0.3 1 808 94 131 765 0.3 1 671 94 132 696 0.3 1 619 77 133 768 0.3 1 705 63 134 1110 0.3 1 1039 71 135 519 0.3 1 468 51 136 251 0.3 1 213 38 137 140 0.3 1 126 14 138 122 0.3 1 106 16 139 85 0.3 1 72 13 140 62 0.3 1 56 6 141 41 0.3 1 39 2 142 38 0.3 1 34 4 143 29 0.3 1 23 6 144 18 0.3 1 9 9 145 46 0.3 1 40 6 146 43 0.3 1 40 3 147 83 0.3 1 73 10 148 54 0.3 1 46 8 149 57 0.3 1 48 9 150 531 0.3 1 439 92 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_L001_R1_001.fastq.gz ============================================= 17274454 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5534 (0.0%)