SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_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/CTRL_16C_26psu_1_S19_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 804.94 s (44 us/read; 1.38 M reads/minute). === Summary === Total reads processed: 18,490,322 Reads with adapters: 14,450,091 (78.1%) Reads written (passing filters): 18,490,322 (100.0%) Total basepairs processed: 2,773,548,300 bp Quality-trimmed: 11,878,254 bp (0.4%) Total written (filtered): 2,174,052,769 bp (78.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14450091 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 12.4% G: 24.6% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2377683 4622580.5 0 2377683 2 369953 1155645.1 0 369953 3 212079 288911.3 0 212079 4 120512 72227.8 0 120512 5 108962 18057.0 0 108962 6 97421 4514.2 0 97421 7 79386 1128.6 0 79386 8 113054 282.1 0 113054 9 87971 70.5 0 87624 347 10 96473 17.6 1 89879 6594 11 101734 4.4 1 93536 8198 12 102089 1.1 1 93747 8342 13 117081 0.3 1 107549 9532 14 108685 0.3 1 98929 9756 15 89117 0.3 1 82133 6984 16 127440 0.3 1 117058 10382 17 108227 0.3 1 99362 8865 18 94672 0.3 1 87210 7462 19 124816 0.3 1 114994 9822 20 116877 0.3 1 108056 8821 21 101808 0.3 1 94028 7780 22 115329 0.3 1 106403 8926 23 122296 0.3 1 112903 9393 24 121720 0.3 1 111954 9766 25 136356 0.3 1 126910 9446 26 113979 0.3 1 104759 9220 27 127054 0.3 1 116622 10432 28 113808 0.3 1 106074 7734 29 126916 0.3 1 117431 9485 30 122281 0.3 1 113729 8552 31 135760 0.3 1 126137 9623 32 117176 0.3 1 109066 8110 33 136110 0.3 1 125744 10366 34 171537 0.3 1 159519 12018 35 95945 0.3 1 89044 6901 36 137046 0.3 1 126917 10129 37 143037 0.3 1 132698 10339 38 133329 0.3 1 124497 8832 39 127534 0.3 1 119434 8100 40 144687 0.3 1 134651 10036 41 140384 0.3 1 131070 9314 42 144299 0.3 1 134780 9519 43 129916 0.3 1 121294 8622 44 151641 0.3 1 141122 10519 45 160400 0.3 1 149699 10701 46 114273 0.3 1 106605 7668 47 144997 0.3 1 136130 8867 48 143166 0.3 1 134124 9042 49 148482 0.3 1 138822 9660 50 140955 0.3 1 131828 9127 51 174978 0.3 1 163816 11162 52 126038 0.3 1 118003 8035 53 153652 0.3 1 144809 8843 54 111499 0.3 1 104710 6789 55 148731 0.3 1 140120 8611 56 152852 0.3 1 143418 9434 57 145621 0.3 1 137708 7913 58 139629 0.3 1 131703 7926 59 139468 0.3 1 131381 8087 60 145979 0.3 1 137374 8605 61 147098 0.3 1 138678 8420 62 160909 0.3 1 151040 9869 63 208484 0.3 1 197875 10609 64 163339 0.3 1 155950 7389 65 115211 0.3 1 108911 6300 66 124628 0.3 1 117681 6947 67 122836 0.3 1 115645 7191 68 124659 0.3 1 117627 7032 69 121178 0.3 1 114114 7064 70 126813 0.3 1 119514 7299 71 132039 0.3 1 124540 7499 72 125242 0.3 1 118005 7237 73 130262 0.3 1 123006 7256 74 119815 0.3 1 112862 6953 75 114051 0.3 1 107533 6518 76 111158 0.3 1 104747 6411 77 111769 0.3 1 105274 6495 78 104990 0.3 1 98882 6108 79 101071 0.3 1 95399 5672 80 100953 0.3 1 95281 5672 81 99176 0.3 1 93590 5586 82 94350 0.3 1 89142 5208 83 91413 0.3 1 86366 5047 84 87258 0.3 1 82554 4704 85 85916 0.3 1 81265 4651 86 84604 0.3 1 80107 4497 87 84396 0.3 1 79885 4511 88 82425 0.3 1 78207 4218 89 73764 0.3 1 69903 3861 90 71339 0.3 1 67438 3901 91 67256 0.3 1 63682 3574 92 62204 0.3 1 58897 3307 93 60201 0.3 1 57003 3198 94 58001 0.3 1 54921 3080 95 54924 0.3 1 52030 2894 96 52451 0.3 1 49666 2785 97 48389 0.3 1 45913 2476 98 44117 0.3 1 41843 2274 99 42086 0.3 1 39795 2291 100 38235 0.3 1 36240 1995 101 35522 0.3 1 33621 1901 102 32226 0.3 1 30512 1714 103 29643 0.3 1 27969 1674 104 28709 0.3 1 27141 1568 105 25222 0.3 1 23921 1301 106 23132 0.3 1 21958 1174 107 20950 0.3 1 19852 1098 108 19130 0.3 1 18127 1003 109 16951 0.3 1 16010 941 110 15532 0.3 1 14697 835 111 14263 0.3 1 13491 772 112 12448 0.3 1 11737 711 113 11105 0.3 1 10532 573 114 9378 0.3 1 8878 500 115 8004 0.3 1 7541 463 116 7028 0.3 1 6643 385 117 5705 0.3 1 5388 317 118 5009 0.3 1 4724 285 119 4196 0.3 1 3948 248 120 3592 0.3 1 3360 232 121 3098 0.3 1 2900 198 122 2572 0.3 1 2409 163 123 2164 0.3 1 2037 127 124 1827 0.3 1 1705 122 125 1543 0.3 1 1435 108 126 1244 0.3 1 1160 84 127 1099 0.3 1 1018 81 128 829 0.3 1 778 51 129 718 0.3 1 677 41 130 539 0.3 1 503 36 131 460 0.3 1 425 35 132 375 0.3 1 343 32 133 337 0.3 1 318 19 134 432 0.3 1 410 22 135 267 0.3 1 250 17 136 145 0.3 1 136 9 137 88 0.3 1 77 11 138 77 0.3 1 69 8 139 43 0.3 1 40 3 140 29 0.3 1 26 3 141 28 0.3 1 23 5 142 25 0.3 1 23 2 143 30 0.3 1 30 144 16 0.3 1 15 1 145 18 0.3 1 15 3 146 29 0.3 1 26 3 147 70 0.3 1 66 4 148 40 0.3 1 37 3 149 46 0.3 1 43 3 150 248 0.3 1 232 16 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_L002_R2_001.fastq.gz ============================================= 18490322 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 19007 (0.1%)