SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L002_R1_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_1_S17_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 567.75 s (42 us/read; 1.44 M reads/minute). === Summary === Total reads processed: 13,627,098 Reads with adapters: 10,357,003 (76.0%) Reads written (passing filters): 13,627,098 (100.0%) Total basepairs processed: 2,044,064,700 bp Quality-trimmed: 4,208,565 bp (0.2%) Total written (filtered): 1,627,255,744 bp (79.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10357003 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.3% C: 15.7% G: 18.6% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2086122 3406774.5 0 2086122 2 266568 851693.6 0 266568 3 152542 212923.4 0 152542 4 89399 53230.9 0 89399 5 70209 13307.7 0 70209 6 66787 3326.9 0 66787 7 53852 831.7 0 53852 8 67948 207.9 0 67948 9 69323 52.0 0 68200 1123 10 63939 13.0 1 59604 4335 11 71265 3.2 1 64858 6407 12 68721 0.8 1 63494 5227 13 67596 0.2 1 62302 5294 14 70216 0.2 1 64057 6159 15 71638 0.2 1 65898 5740 16 71622 0.2 1 65051 6571 17 87796 0.2 1 79687 8109 18 71999 0.2 1 66604 5395 19 63344 0.2 1 58390 4954 20 75324 0.2 1 69407 5917 21 84178 0.2 1 77194 6984 22 70154 0.2 1 65038 5116 23 81908 0.2 1 75394 6514 24 75905 0.2 1 68761 7144 25 81978 0.2 1 75339 6639 26 74054 0.2 1 68713 5341 27 83694 0.2 1 76279 7415 28 82366 0.2 1 75736 6630 29 86579 0.2 1 78687 7892 30 91938 0.2 1 85372 6566 31 70649 0.2 1 65160 5489 32 86162 0.2 1 79280 6882 33 82680 0.2 1 75408 7272 34 100154 0.2 1 90695 9459 35 94358 0.2 1 85860 8498 36 148458 0.2 1 139524 8934 37 35889 0.2 1 31244 4645 38 78400 0.2 1 72661 5739 39 96881 0.2 1 88590 8291 40 92469 0.2 1 85322 7147 41 105619 0.2 1 96453 9166 42 87195 0.2 1 78548 8647 43 141743 0.2 1 132343 9400 44 53443 0.2 1 48101 5342 45 80210 0.2 1 73892 6318 46 94587 0.2 1 87548 7039 47 98921 0.2 1 91675 7246 48 85740 0.2 1 78755 6985 49 103381 0.2 1 94837 8544 50 84900 0.2 1 78738 6162 51 91291 0.2 1 84483 6808 52 97726 0.2 1 89264 8462 53 111539 0.2 1 103945 7594 54 78508 0.2 1 72278 6230 55 97750 0.2 1 90509 7241 56 115622 0.2 1 107685 7937 57 89129 0.2 1 81822 7307 58 92584 0.2 1 86772 5812 59 73435 0.2 1 67515 5920 60 100185 0.2 1 92834 7351 61 93396 0.2 1 86891 6505 62 93505 0.2 1 86821 6684 63 85463 0.2 1 78881 6582 64 86705 0.2 1 80704 6001 65 94221 0.2 1 87522 6699 66 100565 0.2 1 93273 7292 67 109840 0.2 1 100139 9701 68 202049 0.2 1 190563 11486 69 52634 0.2 1 48583 4051 70 17146 0.2 1 14429 2717 71 47197 0.2 1 43653 3544 72 76160 0.2 1 71164 4996 73 81740 0.2 1 76081 5659 74 82050 0.2 1 76332 5718 75 80287 0.2 1 74463 5824 76 79839 0.2 1 73807 6032 77 80016 0.2 1 74278 5738 78 74795 0.2 1 69265 5530 79 74038 0.2 1 68576 5462 80 73576 0.2 1 68130 5446 81 72243 0.2 1 66987 5256 82 69871 0.2 1 64751 5120 83 67762 0.2 1 62929 4833 84 65749 0.2 1 60930 4819 85 64210 0.2 1 59436 4774 86 62228 0.2 1 57683 4545 87 59511 0.2 1 55197 4314 88 59103 0.2 1 54779 4324 89 57029 0.2 1 52911 4118 90 56111 0.2 1 51929 4182 91 53588 0.2 1 49754 3834 92 50869 0.2 1 47115 3754 93 47789 0.2 1 44363 3426 94 47204 0.2 1 43712 3492 95 44549 0.2 1 41263 3286 96 41699 0.2 1 38638 3061 97 39043 0.2 1 36086 2957 98 35735 0.2 1 32882 2853 99 35123 0.2 1 32338 2785 100 32434 0.2 1 30000 2434 101 30205 0.2 1 27895 2310 102 28238 0.2 1 26075 2163 103 26099 0.2 1 24128 1971 104 24785 0.2 1 22897 1888 105 21850 0.2 1 20176 1674 106 20336 0.2 1 18803 1533 107 18435 0.2 1 16991 1444 108 17298 0.2 1 15900 1398 109 15693 0.2 1 14418 1275 110 13857 0.2 1 12707 1150 111 12767 0.2 1 11710 1057 112 11323 0.2 1 10411 912 113 9639 0.2 1 8850 789 114 8830 0.2 1 8052 778 115 7781 0.2 1 7105 676 116 6721 0.2 1 6151 570 117 5849 0.2 1 5270 579 118 5202 0.2 1 4706 496 119 4310 0.2 1 3919 391 120 3867 0.2 1 3492 375 121 3291 0.2 1 2960 331 122 2743 0.2 1 2485 258 123 2310 0.2 1 2091 219 124 2101 0.2 1 1881 220 125 1771 0.2 1 1559 212 126 1539 0.2 1 1390 149 127 1290 0.2 1 1141 149 128 1070 0.2 1 950 120 129 924 0.2 1 833 91 130 685 0.2 1 617 68 131 612 0.2 1 545 67 132 539 0.2 1 487 52 133 666 0.2 1 596 70 134 1493 0.2 1 1414 79 135 574 0.2 1 548 26 136 201 0.2 1 183 18 137 159 0.2 1 145 14 138 108 0.2 1 98 10 139 49 0.2 1 44 5 140 42 0.2 1 38 4 141 43 0.2 1 37 6 142 35 0.2 1 31 4 143 45 0.2 1 39 6 144 56 0.2 1 49 7 145 155 0.2 1 139 16 146 240 0.2 1 219 21 147 1341 0.2 1 1228 113 148 773 0.2 1 707 66 149 433 0.2 1 399 34 150 2986 0.2 1 2547 439 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_1_S17_L002_R1_001.fastq.gz ============================================= 13627098 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 10583 (0.1%)