SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_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_8C_26psu_2_S18_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 616.33 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 16,972,486 Reads with adapters: 15,133,409 (89.2%) Reads written (passing filters): 16,972,486 (100.0%) Total basepairs processed: 2,545,872,900 bp Quality-trimmed: 14,118,915 bp (0.6%) Total written (filtered): 1,669,911,692 bp (65.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15133409 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 991330 4243121.5 0 991330 2 172347 1060780.4 0 172347 3 115382 265195.1 0 115382 4 65389 66298.8 0 65389 5 65284 16574.7 0 65284 6 59675 4143.7 0 59675 7 47228 1035.9 0 47228 8 69329 259.0 0 69329 9 55587 64.7 0 55396 191 10 60044 16.2 1 55911 4133 11 66669 4.0 1 61266 5403 12 66198 1.0 1 60904 5294 13 76711 0.3 1 70697 6014 14 72459 0.3 1 66111 6348 15 58334 0.3 1 54019 4315 16 86573 0.3 1 79901 6672 17 73457 0.3 1 67527 5930 18 65883 0.3 1 60982 4901 19 88155 0.3 1 81417 6738 20 82480 0.3 1 76391 6089 21 74222 0.3 1 68897 5325 22 85010 0.3 1 78866 6144 23 89940 0.3 1 83333 6607 24 90783 0.3 1 83898 6885 25 103545 0.3 1 96553 6992 26 86049 0.3 1 79414 6635 27 97578 0.3 1 89843 7735 28 88487 0.3 1 82899 5588 29 101443 0.3 1 94374 7069 30 98065 0.3 1 91540 6525 31 110927 0.3 1 103494 7433 32 96042 0.3 1 90040 6002 33 113007 0.3 1 105053 7954 34 146678 0.3 1 136868 9810 35 80284 0.3 1 75023 5261 36 119636 0.3 1 111148 8488 37 126797 0.3 1 118353 8444 38 121741 0.3 1 114473 7268 39 116427 0.3 1 109798 6629 40 134566 0.3 1 125810 8756 41 132132 0.3 1 124200 7932 42 135345 0.3 1 127009 8336 43 125343 0.3 1 118018 7325 44 147397 0.3 1 138044 9353 45 153169 0.3 1 143585 9584 46 116858 0.3 1 110003 6855 47 148662 0.3 1 140422 8240 48 146456 0.3 1 138141 8315 49 155663 0.3 1 146241 9422 50 150144 0.3 1 140998 9146 51 186605 0.3 1 175426 11179 52 135487 0.3 1 127796 7691 53 169781 0.3 1 161047 8734 54 125345 0.3 1 118710 6635 55 168692 0.3 1 160003 8689 56 176257 0.3 1 166258 9999 57 169891 0.3 1 161571 8320 58 164276 0.3 1 156000 8276 59 168462 0.3 1 159572 8890 60 177599 0.3 1 168506 9093 61 183440 0.3 1 174203 9237 62 202372 0.3 1 191386 10986 63 270936 0.3 1 258181 12755 64 234996 0.3 1 225774 9222 65 151631 0.3 1 144050 7581 66 166302 0.3 1 157972 8330 67 167833 0.3 1 159201 8632 68 170330 0.3 1 161782 8548 69 171332 0.3 1 162512 8820 70 183649 0.3 1 174535 9114 71 199117 0.3 1 189420 9697 72 190292 0.3 1 180708 9584 73 205025 0.3 1 195024 10001 74 188852 0.3 1 179445 9407 75 181257 0.3 1 172280 8977 76 178734 0.3 1 169881 8853 77 180452 0.3 1 171277 9175 78 172679 0.3 1 164051 8628 79 170532 0.3 1 162087 8445 80 171521 0.3 1 163340 8181 81 171140 0.3 1 162630 8510 82 165207 0.3 1 157233 7974 83 163608 0.3 1 155825 7783 84 160013 0.3 1 152625 7388 85 159454 0.3 1 151925 7529 86 161481 0.3 1 153907 7574 87 162581 0.3 1 155126 7455 88 162054 0.3 1 154673 7381 89 147788 0.3 1 141132 6656 90 145172 0.3 1 138698 6474 91 139015 0.3 1 132745 6270 92 132299 0.3 1 126316 5983 93 128552 0.3 1 122735 5817 94 126711 0.3 1 120900 5811 95 119947 0.3 1 114454 5493 96 117162 0.3 1 111939 5223 97 108989 0.3 1 104182 4807 98 105848 0.3 1 101282 4566 99 105989 0.3 1 101349 4640 100 98144 0.3 1 93908 4236 101 94920 0.3 1 90864 4056 102 89211 0.3 1 85259 3952 103 81188 0.3 1 77654 3534 104 77565 0.3 1 74081 3484 105 70248 0.3 1 67249 2999 106 65288 0.3 1 62604 2684 107 60022 0.3 1 57428 2594 108 55515 0.3 1 53019 2496 109 50990 0.3 1 48728 2262 110 46869 0.3 1 44831 2038 111 44489 0.3 1 42630 1859 112 39619 0.3 1 37888 1731 113 34543 0.3 1 33015 1528 114 31368 0.3 1 30023 1345 115 26935 0.3 1 25774 1161 116 23611 0.3 1 22614 997 117 19912 0.3 1 18993 919 118 17572 0.3 1 16789 783 119 14871 0.3 1 14194 677 120 12844 0.3 1 12244 600 121 11858 0.3 1 11313 545 122 9930 0.3 1 9463 467 123 8753 0.3 1 8342 411 124 7126 0.3 1 6812 314 125 6158 0.3 1 5890 268 126 5177 0.3 1 4954 223 127 4434 0.3 1 4233 201 128 3338 0.3 1 3185 153 129 2850 0.3 1 2742 108 130 2111 0.3 1 2001 110 131 1887 0.3 1 1807 80 132 1727 0.3 1 1658 69 133 2467 0.3 1 2378 89 134 4553 0.3 1 4401 152 135 1770 0.3 1 1714 56 136 598 0.3 1 559 39 137 389 0.3 1 374 15 138 283 0.3 1 271 12 139 188 0.3 1 181 7 140 133 0.3 1 124 9 141 75 0.3 1 73 2 142 64 0.3 1 61 3 143 64 0.3 1 59 5 144 68 0.3 1 66 2 145 139 0.3 1 132 7 146 159 0.3 1 151 8 147 678 0.3 1 647 31 148 467 0.3 1 450 17 149 278 0.3 1 263 15 150 2366 0.3 1 2224 142 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_L002_R2_001.fastq.gz ============================================= 16972486 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 39693 (0.2%)