SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_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/CTRL_8C_26psu_2_S18_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 579.26 s (34 us/read; 1.76 M reads/minute). === Summary === Total reads processed: 16,982,389 Reads with adapters: 15,316,406 (90.2%) Reads written (passing filters): 16,982,389 (100.0%) Total basepairs processed: 2,547,358,350 bp Quality-trimmed: 5,122,052 bp (0.2%) Total written (filtered): 1,661,718,543 bp (65.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15316406 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 17.9% G: 21.3% T: 32.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 934198 4245597.2 0 934198 2 161909 1061399.3 0 161909 3 105071 265349.8 0 105071 4 65361 66337.5 0 65361 5 61151 16584.4 0 61151 6 60130 4146.1 0 60130 7 51265 1036.5 0 51265 8 64755 259.1 0 64755 9 64351 64.8 0 63580 771 10 61337 16.2 1 58020 3317 11 70221 4.0 1 64705 5516 12 66216 1.0 1 61889 4327 13 69137 0.3 1 64630 4507 14 70780 0.3 1 65742 5038 15 75204 0.3 1 70097 5107 16 73779 0.3 1 68019 5760 17 90043 0.3 1 82540 7503 18 81214 0.3 1 76392 4822 19 66550 0.3 1 62390 4160 20 83867 0.3 1 78220 5647 21 92423 0.3 1 86031 6392 22 79989 0.3 1 75306 4683 23 93784 0.3 1 87424 6360 24 89031 0.3 1 81718 7313 25 96197 0.3 1 89537 6660 26 88926 0.3 1 83710 5216 27 100077 0.3 1 92668 7409 28 100613 0.3 1 93553 7060 29 104938 0.3 1 96491 8447 30 117488 0.3 1 110880 6608 31 89018 0.3 1 83492 5526 32 107667 0.3 1 100716 6951 33 110564 0.3 1 102547 8017 34 137673 0.3 1 127216 10457 35 119092 0.3 1 112273 6819 36 94075 0.3 1 88092 5983 37 125638 0.3 1 116775 8863 38 138305 0.3 1 128145 10160 39 120373 0.3 1 113314 7059 40 138522 0.3 1 128397 10125 41 158012 0.3 1 146728 11284 42 111371 0.3 1 103118 8253 43 217278 0.3 1 206218 11060 44 57407 0.3 1 51985 5422 45 143497 0.3 1 134258 9239 46 142849 0.3 1 133725 9124 47 147972 0.3 1 139076 8896 48 148858 0.3 1 138933 9925 49 163896 0.3 1 152740 11156 50 140197 0.3 1 131951 8246 51 154425 0.3 1 144692 9733 52 163399 0.3 1 151525 11874 53 181558 0.3 1 170911 10647 54 136765 0.3 1 128031 8734 55 172905 0.3 1 161877 11028 56 211987 0.3 1 200164 11823 57 138899 0.3 1 129027 9872 58 181048 0.3 1 171675 9373 59 152882 0.3 1 143208 9674 60 179132 0.3 1 167976 11156 61 179957 0.3 1 169292 10665 62 195431 0.3 1 184537 10894 63 158140 0.3 1 148011 10129 64 177885 0.3 1 167763 10122 65 200563 0.3 1 188662 11901 66 211859 0.3 1 199050 12809 67 228942 0.3 1 211658 17284 68 447452 0.3 1 426829 20623 69 83220 0.3 1 76361 6859 70 30543 0.3 1 25376 5167 71 119720 0.3 1 112578 7142 72 172151 0.3 1 162467 9684 73 185670 0.3 1 174903 10767 74 186107 0.3 1 175086 11021 75 187142 0.3 1 176040 11102 76 187583 0.3 1 176804 10779 77 190166 0.3 1 178927 11239 78 180337 0.3 1 169693 10644 79 182061 0.3 1 171352 10709 80 179279 0.3 1 168912 10367 81 180871 0.3 1 170399 10472 82 177227 0.3 1 166777 10450 83 175671 0.3 1 165379 10292 84 171899 0.3 1 161834 10065 85 167562 0.3 1 157917 9645 86 164690 0.3 1 155117 9573 87 159808 0.3 1 150364 9444 88 160575 0.3 1 151109 9466 89 154675 0.3 1 145660 9015 90 155657 0.3 1 146266 9391 91 151129 0.3 1 142165 8964 92 144841 0.3 1 136295 8546 93 137285 0.3 1 129298 7987 94 135380 0.3 1 127295 8085 95 127081 0.3 1 119343 7738 96 122579 0.3 1 115210 7369 97 117441 0.3 1 110330 7111 98 110426 0.3 1 103591 6835 99 109189 0.3 1 102159 7030 100 100853 0.3 1 94763 6090 101 96345 0.3 1 90423 5922 102 89845 0.3 1 84149 5696 103 85390 0.3 1 80150 5240 104 79941 0.3 1 74924 5017 105 72924 0.3 1 68266 4658 106 67356 0.3 1 63014 4342 107 62697 0.3 1 58614 4083 108 60572 0.3 1 56580 3992 109 54023 0.3 1 50378 3645 110 49550 0.3 1 46112 3438 111 45365 0.3 1 42247 3118 112 40518 0.3 1 37628 2890 113 35484 0.3 1 32846 2638 114 32042 0.3 1 29706 2336 115 28111 0.3 1 26004 2107 116 25248 0.3 1 23329 1919 117 21991 0.3 1 20192 1799 118 18981 0.3 1 17374 1607 119 16315 0.3 1 14943 1372 120 14190 0.3 1 13063 1127 121 12626 0.3 1 11644 982 122 10330 0.3 1 9443 887 123 9025 0.3 1 8218 807 124 7634 0.3 1 6995 639 125 6434 0.3 1 5834 600 126 5520 0.3 1 5002 518 127 4681 0.3 1 4249 432 128 3676 0.3 1 3257 419 129 3146 0.3 1 2839 307 130 2431 0.3 1 2189 242 131 2160 0.3 1 1904 256 132 1916 0.3 1 1719 197 133 2331 0.3 1 2120 211 134 4696 0.3 1 4441 255 135 1717 0.3 1 1602 115 136 624 0.3 1 562 62 137 434 0.3 1 390 44 138 279 0.3 1 239 40 139 193 0.3 1 171 22 140 139 0.3 1 121 18 141 116 0.3 1 101 15 142 99 0.3 1 87 12 143 71 0.3 1 56 15 144 68 0.3 1 49 19 145 142 0.3 1 121 21 146 149 0.3 1 136 13 147 732 0.3 1 658 74 148 489 0.3 1 451 38 149 276 0.3 1 251 25 150 3068 0.3 1 2637 431 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_L001_R1_001.fastq.gz ============================================= 16982389 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 19765 (0.1%)