SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_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/16C_26psu_4_S16_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 728.62 s (42 us/read; 1.42 M reads/minute). === Summary === Total reads processed: 17,208,353 Reads with adapters: 13,587,185 (79.0%) Reads written (passing filters): 17,208,353 (100.0%) Total basepairs processed: 2,581,252,950 bp Quality-trimmed: 13,418,385 bp (0.5%) Total written (filtered): 1,981,075,586 bp (76.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13587185 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.8% C: 13.6% G: 24.4% T: 34.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2180320 4302088.2 0 2180320 2 324825 1075522.1 0 324825 3 196027 268880.5 0 196027 4 105938 67220.1 0 105938 5 93022 16805.0 0 93022 6 82169 4201.3 0 82169 7 65208 1050.3 0 65208 8 94076 262.6 0 94076 9 75651 65.6 0 75373 278 10 79743 16.4 1 74241 5502 11 88328 4.1 1 81010 7318 12 86868 1.0 1 79554 7314 13 99881 0.3 1 91747 8134 14 90834 0.3 1 82543 8291 15 75785 0.3 1 69708 6077 16 109506 0.3 1 100461 9045 17 89706 0.3 1 82164 7542 18 82342 0.3 1 75779 6563 19 105511 0.3 1 97019 8492 20 99413 0.3 1 91913 7500 21 89589 0.3 1 82387 7202 22 99486 0.3 1 91727 7759 23 104499 0.3 1 96352 8147 24 104372 0.3 1 95967 8405 25 118405 0.3 1 110027 8378 26 97628 0.3 1 89447 8181 27 110575 0.3 1 101151 9424 28 97751 0.3 1 91186 6565 29 111505 0.3 1 102881 8624 30 104420 0.3 1 97112 7308 31 118911 0.3 1 110316 8595 32 102066 0.3 1 95076 6990 33 118362 0.3 1 109639 8723 34 152523 0.3 1 141524 10999 35 81147 0.3 1 75248 5899 36 120338 0.3 1 111218 9120 37 127944 0.3 1 118775 9169 38 118773 0.3 1 111107 7666 39 114524 0.3 1 107290 7234 40 130962 0.3 1 121798 9164 41 127042 0.3 1 118718 8324 42 130066 0.3 1 121378 8688 43 114447 0.3 1 107009 7438 44 134439 0.3 1 125115 9324 45 139316 0.3 1 130061 9255 46 105889 0.3 1 98943 6946 47 133294 0.3 1 125179 8115 48 129000 0.3 1 120992 8008 49 134472 0.3 1 125771 8701 50 129511 0.3 1 120901 8610 51 156322 0.3 1 146348 9974 52 115554 0.3 1 108318 7236 53 141127 0.3 1 132995 8132 54 105383 0.3 1 99036 6347 55 137072 0.3 1 129093 7979 56 141674 0.3 1 132689 8985 57 134402 0.3 1 126942 7460 58 130317 0.3 1 123061 7256 59 129827 0.3 1 122170 7657 60 136682 0.3 1 128763 7919 61 138438 0.3 1 130627 7811 62 151584 0.3 1 142493 9091 63 198913 0.3 1 188533 10380 64 165224 0.3 1 157788 7436 65 109943 0.3 1 103886 6057 66 119196 0.3 1 112621 6575 67 118137 0.3 1 111336 6801 68 119874 0.3 1 113325 6549 69 119266 0.3 1 112294 6972 70 126609 0.3 1 119544 7065 71 132620 0.3 1 125297 7323 72 125393 0.3 1 118453 6940 73 132184 0.3 1 124866 7318 74 122169 0.3 1 115334 6835 75 116493 0.3 1 110071 6422 76 113442 0.3 1 106974 6468 77 113685 0.3 1 107141 6544 78 108607 0.3 1 102395 6212 79 104353 0.3 1 98543 5810 80 104020 0.3 1 98279 5741 81 102310 0.3 1 96699 5611 82 98054 0.3 1 92664 5390 83 96480 0.3 1 91293 5187 84 93016 0.3 1 87985 5031 85 91834 0.3 1 86918 4916 86 92118 0.3 1 87322 4796 87 91952 0.3 1 87281 4671 88 89832 0.3 1 85225 4607 89 81915 0.3 1 77620 4295 90 78846 0.3 1 74588 4258 91 74284 0.3 1 70441 3843 92 69858 0.3 1 66293 3565 93 66592 0.3 1 63127 3465 94 65539 0.3 1 62049 3490 95 61188 0.3 1 57883 3305 96 59534 0.3 1 56516 3018 97 56011 0.3 1 53174 2837 98 53355 0.3 1 50647 2708 99 53101 0.3 1 50373 2728 100 48195 0.3 1 45837 2358 101 43522 0.3 1 41188 2334 102 41863 0.3 1 39765 2098 103 39452 0.3 1 37477 1975 104 38339 0.3 1 36409 1930 105 33606 0.3 1 31895 1711 106 30952 0.3 1 29448 1504 107 27675 0.3 1 26330 1345 108 24951 0.3 1 23635 1316 109 22743 0.3 1 21560 1183 110 20811 0.3 1 19684 1127 111 19926 0.3 1 18958 968 112 17187 0.3 1 16283 904 113 15096 0.3 1 14331 765 114 13260 0.3 1 12650 610 115 11435 0.3 1 10854 581 116 9981 0.3 1 9425 556 117 8327 0.3 1 7873 454 118 7364 0.3 1 6994 370 119 6240 0.3 1 5915 325 120 5208 0.3 1 4920 288 121 4741 0.3 1 4467 274 122 4055 0.3 1 3851 204 123 3533 0.3 1 3332 201 124 2985 0.3 1 2813 172 125 2559 0.3 1 2417 142 126 2133 0.3 1 2012 121 127 1706 0.3 1 1579 127 128 1327 0.3 1 1241 86 129 1121 0.3 1 1038 83 130 901 0.3 1 842 59 131 784 0.3 1 738 46 132 657 0.3 1 620 37 133 809 0.3 1 770 39 134 1081 0.3 1 1031 50 135 490 0.3 1 465 25 136 231 0.3 1 213 18 137 165 0.3 1 153 12 138 122 0.3 1 117 5 139 68 0.3 1 64 4 140 60 0.3 1 53 7 141 31 0.3 1 25 6 142 34 0.3 1 30 4 143 37 0.3 1 30 7 144 24 0.3 1 20 4 145 49 0.3 1 45 4 146 39 0.3 1 34 5 147 87 0.3 1 77 10 148 52 0.3 1 48 4 149 25 0.3 1 23 2 150 408 0.3 1 378 30 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_L002_R2_001.fastq.gz ============================================= 17208353 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 27317 (0.2%)