SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_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_1_S19_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 791.42 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 18,576,202 Reads with adapters: 14,527,088 (78.2%) Reads written (passing filters): 18,576,202 (100.0%) Total basepairs processed: 2,786,430,300 bp Quality-trimmed: 12,297,720 bp (0.4%) Total written (filtered): 2,186,026,388 bp (78.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14527088 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 12.4% G: 24.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2397075 4644050.5 0 2397075 2 377772 1161012.6 0 377772 3 209931 290253.2 0 209931 4 123717 72563.3 0 123717 5 112624 18140.8 0 112624 6 97477 4535.2 0 97477 7 81404 1133.8 0 81404 8 114796 283.5 0 114796 9 89736 70.9 0 89386 350 10 100021 17.7 1 95112 4909 11 103726 4.4 1 97357 6369 12 104603 1.1 1 97938 6665 13 116572 0.3 1 109738 6834 14 110440 0.3 1 102780 7660 15 91038 0.3 1 85192 5846 16 129548 0.3 1 121431 8117 17 105093 0.3 1 97969 7124 18 99076 0.3 1 93067 6009 19 126890 0.3 1 118635 8255 20 118457 0.3 1 111491 6966 21 103736 0.3 1 97365 6371 22 118151 0.3 1 110881 7270 23 121946 0.3 1 114464 7482 24 121962 0.3 1 114186 7776 25 136854 0.3 1 128708 8146 26 113321 0.3 1 106068 7253 27 126381 0.3 1 117798 8583 28 118846 0.3 1 112727 6119 29 125505 0.3 1 117793 7712 30 125215 0.3 1 118459 6756 31 135187 0.3 1 127291 7896 32 121491 0.3 1 114900 6591 33 135254 0.3 1 127041 8213 34 169655 0.3 1 159717 9938 35 101342 0.3 1 95776 5566 36 136505 0.3 1 128363 8142 37 143293 0.3 1 134875 8418 38 134051 0.3 1 127357 6694 39 131563 0.3 1 124738 6825 40 145300 0.3 1 136735 8565 41 138947 0.3 1 131652 7295 42 144334 0.3 1 136660 7674 43 131871 0.3 1 124782 7089 44 149402 0.3 1 141199 8203 45 161283 0.3 1 152880 8403 46 115740 0.3 1 109551 6189 47 146650 0.3 1 139277 7373 48 144979 0.3 1 137763 7216 49 149370 0.3 1 141741 7629 50 140556 0.3 1 132993 7563 51 176763 0.3 1 167628 9135 52 125327 0.3 1 119270 6057 53 150468 0.3 1 143751 6717 54 114488 0.3 1 108938 5550 55 150264 0.3 1 143436 6828 56 154642 0.3 1 147075 7567 57 145698 0.3 1 138895 6803 58 139003 0.3 1 132772 6231 59 141639 0.3 1 135020 6619 60 145216 0.3 1 138147 7069 61 149173 0.3 1 141978 7195 62 161580 0.3 1 153777 7803 63 211777 0.3 1 202721 9056 64 166013 0.3 1 159545 6468 65 115072 0.3 1 109927 5145 66 124032 0.3 1 118392 5640 67 121997 0.3 1 116256 5741 68 123305 0.3 1 117689 5616 69 119979 0.3 1 114424 5555 70 126522 0.3 1 120645 5877 71 131428 0.3 1 125503 5925 72 124583 0.3 1 118750 5833 73 129753 0.3 1 124066 5687 74 119016 0.3 1 113726 5290 75 113191 0.3 1 108419 4772 76 111393 0.3 1 106547 4846 77 111470 0.3 1 106513 4957 78 104799 0.3 1 100049 4750 79 100883 0.3 1 96421 4462 80 100236 0.3 1 95706 4530 81 98928 0.3 1 94651 4277 82 94279 0.3 1 90155 4124 83 90115 0.3 1 86173 3942 84 87249 0.3 1 83373 3876 85 85689 0.3 1 81793 3896 86 84888 0.3 1 81207 3681 87 84171 0.3 1 80558 3613 88 82226 0.3 1 78630 3596 89 73279 0.3 1 70084 3195 90 71368 0.3 1 68189 3179 91 66468 0.3 1 63502 2966 92 61869 0.3 1 59204 2665 93 59677 0.3 1 57086 2591 94 57840 0.3 1 55318 2522 95 54875 0.3 1 52595 2280 96 51698 0.3 1 49449 2249 97 47519 0.3 1 45519 2000 98 43527 0.3 1 41676 1851 99 42094 0.3 1 40263 1831 100 37940 0.3 1 36384 1556 101 34646 0.3 1 33175 1471 102 32213 0.3 1 30921 1292 103 29202 0.3 1 27960 1242 104 28501 0.3 1 27313 1188 105 25308 0.3 1 24224 1084 106 22773 0.3 1 21858 915 107 20894 0.3 1 20051 843 108 18912 0.3 1 18081 831 109 17072 0.3 1 16336 736 110 15374 0.3 1 14700 674 111 14518 0.3 1 13895 623 112 12456 0.3 1 11891 565 113 10771 0.3 1 10329 442 114 9374 0.3 1 8976 398 115 7920 0.3 1 7555 365 116 6787 0.3 1 6458 329 117 5803 0.3 1 5538 265 118 4857 0.3 1 4636 221 119 4060 0.3 1 3861 199 120 3400 0.3 1 3228 172 121 3132 0.3 1 2976 156 122 2609 0.3 1 2493 116 123 2165 0.3 1 2072 93 124 1770 0.3 1 1676 94 125 1516 0.3 1 1432 84 126 1213 0.3 1 1153 60 127 1001 0.3 1 941 60 128 776 0.3 1 728 48 129 744 0.3 1 699 45 130 486 0.3 1 463 23 131 460 0.3 1 438 22 132 343 0.3 1 315 28 133 355 0.3 1 338 17 134 428 0.3 1 403 25 135 226 0.3 1 216 10 136 133 0.3 1 120 13 137 125 0.3 1 117 8 138 70 0.3 1 62 8 139 38 0.3 1 35 3 140 38 0.3 1 31 7 141 35 0.3 1 33 2 142 27 0.3 1 26 1 143 32 0.3 1 30 2 144 14 0.3 1 13 1 145 17 0.3 1 16 1 146 23 0.3 1 23 147 69 0.3 1 65 4 148 40 0.3 1 38 2 149 38 0.3 1 34 4 150 229 0.3 1 219 10 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_1_S19_L001_R2_001.fastq.gz ============================================= 18576202 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 20489 (0.1%)