SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_L001_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_2_S21_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 516.35 s (38 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 13,433,110 Reads with adapters: 11,642,556 (86.7%) Reads written (passing filters): 13,433,110 (100.0%) Total basepairs processed: 2,014,966,500 bp Quality-trimmed: 8,709,221 bp (0.4%) Total written (filtered): 1,432,856,177 bp (71.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11642556 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 11.7% G: 26.2% T: 34.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1015848 3358277.5 0 1015848 2 179924 839569.4 0 179924 3 110740 209892.3 0 110740 4 68288 52473.1 0 68288 5 68265 13118.3 0 68265 6 61219 3279.6 0 61219 7 51190 819.9 0 51190 8 71859 205.0 0 71859 9 56699 51.2 0 56454 245 10 63956 12.8 1 61051 2905 11 67245 3.2 1 63190 4055 12 68588 0.8 1 64563 4025 13 77409 0.2 1 73173 4236 14 74943 0.2 1 70185 4758 15 61575 0.2 1 58112 3463 16 87672 0.2 1 82660 5012 17 73552 0.2 1 68954 4598 18 68802 0.2 1 65063 3739 19 88259 0.2 1 82939 5320 20 82556 0.2 1 78141 4415 21 73225 0.2 1 69045 4180 22 83863 0.2 1 79245 4618 23 87811 0.2 1 82813 4998 24 89014 0.2 1 83968 5046 25 100238 0.2 1 94973 5265 26 83574 0.2 1 78786 4788 27 93033 0.2 1 87412 5621 28 89387 0.2 1 85387 4000 29 95696 0.2 1 90729 4967 30 94787 0.2 1 90441 4346 31 102169 0.2 1 97061 5108 32 94007 0.2 1 89720 4287 33 105833 0.2 1 100418 5415 34 134739 0.2 1 127847 6892 35 80075 0.2 1 76383 3692 36 104516 0.2 1 98895 5621 37 113410 0.2 1 107671 5739 38 107520 0.2 1 102889 4631 39 105637 0.2 1 101025 4612 40 118785 0.2 1 112992 5793 41 115631 0.2 1 110394 5237 42 122110 0.2 1 116550 5560 43 111230 0.2 1 106271 4959 44 128541 0.2 1 122788 5753 45 137963 0.2 1 131813 6150 46 99340 0.2 1 94897 4443 47 125922 0.2 1 120367 5555 48 125595 0.2 1 120423 5172 49 132842 0.2 1 126935 5907 50 127676 0.2 1 122004 5672 51 163515 0.2 1 156244 7271 52 117884 0.2 1 113079 4805 53 142736 0.2 1 137315 5421 54 107101 0.2 1 102800 4301 55 139222 0.2 1 133903 5319 56 143656 0.2 1 137859 5797 57 140073 0.2 1 134871 5202 58 134625 0.2 1 129700 4925 59 134950 0.2 1 129802 5148 60 140295 0.2 1 134781 5514 61 144854 0.2 1 139165 5689 62 159948 0.2 1 153492 6456 63 215119 0.2 1 207339 7780 64 166765 0.2 1 161464 5301 65 114876 0.2 1 110601 4275 66 125878 0.2 1 121273 4605 67 126455 0.2 1 121514 4941 68 128071 0.2 1 123304 4767 69 126908 0.2 1 122039 4869 70 132340 0.2 1 127378 4962 71 137419 0.2 1 132563 4856 72 133254 0.2 1 128394 4860 73 140768 0.2 1 135639 5129 74 130186 0.2 1 125634 4552 75 123476 0.2 1 119176 4300 76 121581 0.2 1 117266 4315 77 120182 0.2 1 115605 4577 78 115742 0.2 1 111521 4221 79 111421 0.2 1 107330 4091 80 110726 0.2 1 106773 3953 81 109599 0.2 1 105677 3922 82 103036 0.2 1 99365 3671 83 100716 0.2 1 97173 3543 84 98439 0.2 1 94811 3628 85 96847 0.2 1 93310 3537 86 96817 0.2 1 93338 3479 87 95905 0.2 1 92582 3323 88 93526 0.2 1 90163 3363 89 83831 0.2 1 80785 3046 90 80158 0.2 1 77319 2839 91 74964 0.2 1 72203 2761 92 70024 0.2 1 67553 2471 93 68027 0.2 1 65623 2404 94 64372 0.2 1 62143 2229 95 61456 0.2 1 59284 2172 96 57585 0.2 1 55560 2025 97 53463 0.2 1 51605 1858 98 50229 0.2 1 48488 1741 99 48358 0.2 1 46710 1648 100 43743 0.2 1 42301 1442 101 39334 0.2 1 37976 1358 102 35681 0.2 1 34444 1237 103 32169 0.2 1 31042 1127 104 30344 0.2 1 29354 990 105 26673 0.2 1 25747 926 106 24610 0.2 1 23753 857 107 21493 0.2 1 20733 760 108 19129 0.2 1 18449 680 109 17216 0.2 1 16604 612 110 15680 0.2 1 15121 559 111 14422 0.2 1 13916 506 112 12048 0.2 1 11652 396 113 10682 0.2 1 10293 389 114 9191 0.2 1 8830 361 115 7355 0.2 1 7077 278 116 6245 0.2 1 6016 229 117 5167 0.2 1 4936 231 118 4511 0.2 1 4330 181 119 3552 0.2 1 3385 167 120 3201 0.2 1 3062 139 121 2450 0.2 1 2343 107 122 2029 0.2 1 1935 94 123 1814 0.2 1 1715 99 124 1524 0.2 1 1436 88 125 1206 0.2 1 1139 67 126 1198 0.2 1 1135 63 127 925 0.2 1 875 50 128 706 0.2 1 663 43 129 633 0.2 1 590 43 130 698 0.2 1 666 32 131 844 0.2 1 815 29 132 910 0.2 1 876 34 133 1412 0.2 1 1368 44 134 1698 0.2 1 1641 57 135 718 0.2 1 696 22 136 190 0.2 1 177 13 137 107 0.2 1 98 9 138 70 0.2 1 67 3 139 53 0.2 1 50 3 140 53 0.2 1 52 1 141 26 0.2 1 26 142 26 0.2 1 24 2 143 21 0.2 1 20 1 144 18 0.2 1 16 2 145 35 0.2 1 32 3 146 39 0.2 1 35 4 147 177 0.2 1 169 8 148 82 0.2 1 76 6 149 45 0.2 1 43 2 150 267 0.2 1 241 26 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_L001_R2_001.fastq.gz ============================================= 13433110 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 18598 (0.1%)