SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_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_8C_26psu_2_S18_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 602.01 s (35 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 16,982,389 Reads with adapters: 15,175,955 (89.4%) Reads written (passing filters): 16,982,389 (100.0%) Total basepairs processed: 2,547,358,350 bp Quality-trimmed: 14,637,859 bp (0.6%) Total written (filtered): 1,670,081,107 bp (65.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15175955 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.2% C: 14.2% G: 26.5% T: 33.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 988355 4245597.2 0 988355 2 174327 1061399.3 0 174327 3 112326 265349.8 0 112326 4 66944 66337.5 0 66944 5 68049 16584.4 0 68049 6 59622 4146.1 0 59622 7 48077 1036.5 0 48077 8 70632 259.1 0 70632 9 56419 64.8 0 56220 199 10 62892 16.2 1 59906 2986 11 67246 4.0 1 63200 4046 12 67488 1.0 1 63307 4181 13 76798 0.3 1 72553 4245 14 73938 0.3 1 68873 5065 15 59370 0.3 1 55860 3510 16 87943 0.3 1 82783 5160 17 71376 0.3 1 66695 4681 18 68792 0.3 1 64885 3907 19 88616 0.3 1 83090 5526 20 83852 0.3 1 79094 4758 21 75082 0.3 1 70636 4446 22 86387 0.3 1 81609 4778 23 90257 0.3 1 85055 5202 24 90691 0.3 1 85295 5396 25 104055 0.3 1 98264 5791 26 86753 0.3 1 81712 5041 27 96821 0.3 1 90516 6305 28 92589 0.3 1 88280 4309 29 100006 0.3 1 94283 5723 30 100693 0.3 1 95722 4971 31 110238 0.3 1 104335 5903 32 99509 0.3 1 94661 4848 33 112333 0.3 1 106128 6205 34 145441 0.3 1 137472 7969 35 84427 0.3 1 80249 4178 36 119286 0.3 1 112593 6693 37 127293 0.3 1 120329 6964 38 123047 0.3 1 117261 5786 39 119775 0.3 1 114281 5494 40 135696 0.3 1 128262 7434 41 130689 0.3 1 124366 6323 42 135604 0.3 1 129108 6496 43 126835 0.3 1 120741 6094 44 146922 0.3 1 139741 7181 45 154339 0.3 1 146909 7430 46 118308 0.3 1 112832 5476 47 149295 0.3 1 142485 6810 48 148606 0.3 1 142089 6517 49 156890 0.3 1 149693 7197 50 148375 0.3 1 141320 7055 51 190171 0.3 1 181254 8917 52 136804 0.3 1 130968 5836 53 165906 0.3 1 159264 6642 54 128157 0.3 1 122871 5286 55 169343 0.3 1 162704 6639 56 177473 0.3 1 169804 7669 57 169211 0.3 1 162646 6565 58 164197 0.3 1 158052 6145 59 169249 0.3 1 162429 6820 60 177455 0.3 1 170133 7322 61 185762 0.3 1 177933 7829 62 204728 0.3 1 196280 8448 63 277535 0.3 1 267196 10339 64 238674 0.3 1 230905 7769 65 152399 0.3 1 146631 5768 66 166909 0.3 1 160634 6275 67 166804 0.3 1 160075 6729 68 169255 0.3 1 162913 6342 69 169940 0.3 1 163142 6798 70 182641 0.3 1 175571 7070 71 198941 0.3 1 191661 7280 72 188343 0.3 1 181180 7163 73 204850 0.3 1 197436 7414 74 188381 0.3 1 181668 6713 75 180633 0.3 1 173941 6692 76 178500 0.3 1 172078 6422 77 180330 0.3 1 173546 6784 78 173641 0.3 1 167180 6461 79 170287 0.3 1 164090 6197 80 170838 0.3 1 164653 6185 81 172175 0.3 1 165934 6241 82 165553 0.3 1 159555 5998 83 164742 0.3 1 158792 5950 84 160682 0.3 1 154778 5904 85 159281 0.3 1 153367 5914 86 160523 0.3 1 154638 5885 87 163301 0.3 1 157413 5888 88 161676 0.3 1 155871 5805 89 147453 0.3 1 142105 5348 90 143818 0.3 1 138625 5193 91 138225 0.3 1 133103 5122 92 131088 0.3 1 126317 4771 93 128053 0.3 1 123615 4438 94 125505 0.3 1 121074 4431 95 119294 0.3 1 114964 4330 96 116155 0.3 1 112159 3996 97 108812 0.3 1 105094 3718 98 104976 0.3 1 101373 3603 99 105895 0.3 1 102281 3614 100 97778 0.3 1 94611 3167 101 95386 0.3 1 92351 3035 102 88691 0.3 1 85785 2906 103 80552 0.3 1 77853 2699 104 77505 0.3 1 74941 2564 105 70382 0.3 1 68000 2382 106 65184 0.3 1 63051 2133 107 60057 0.3 1 58146 1911 108 55681 0.3 1 53827 1854 109 50629 0.3 1 48896 1733 110 46572 0.3 1 45046 1526 111 44577 0.3 1 43131 1446 112 39344 0.3 1 38114 1230 113 34530 0.3 1 33382 1148 114 30993 0.3 1 30031 962 115 26355 0.3 1 25472 883 116 23180 0.3 1 22328 852 117 19825 0.3 1 19141 684 118 17184 0.3 1 16546 638 119 14938 0.3 1 14436 502 120 12856 0.3 1 12387 469 121 11667 0.3 1 11246 421 122 9613 0.3 1 9258 355 123 8582 0.3 1 8274 308 124 7156 0.3 1 6897 259 125 6130 0.3 1 5897 233 126 5195 0.3 1 5039 156 127 4372 0.3 1 4226 146 128 3397 0.3 1 3245 152 129 2899 0.3 1 2785 114 130 2231 0.3 1 2140 91 131 2005 0.3 1 1925 80 132 1815 0.3 1 1740 75 133 2411 0.3 1 2321 90 134 4708 0.3 1 4577 131 135 1657 0.3 1 1601 56 136 589 0.3 1 574 15 137 406 0.3 1 391 15 138 265 0.3 1 252 13 139 182 0.3 1 175 7 140 132 0.3 1 124 8 141 111 0.3 1 106 5 142 101 0.3 1 96 5 143 63 0.3 1 60 3 144 61 0.3 1 57 4 145 160 0.3 1 154 6 146 146 0.3 1 139 7 147 687 0.3 1 666 21 148 439 0.3 1 426 13 149 260 0.3 1 251 9 150 2448 0.3 1 2325 123 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_L001_R2_001.fastq.gz ============================================= 16982389 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 41433 (0.2%)