SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 7650.23 s (25 us/read; 2.43 M reads/minute). === Summary === Total reads processed: 309,877,704 Reads with adapters: 125,600,847 (40.5%) Reads written (passing filters): 309,877,704 (100.0%) Total basepairs processed: 39,009,495,129 bp Quality-trimmed: 24,971,797 bp (0.1%) Total written (filtered): 38,552,981,389 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 125600847 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.1% C: 23.7% G: 14.5% T: 29.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 89424517 77469426.0 0 89424517 2 22164935 19367356.5 0 22164935 3 6130509 4841839.1 0 6130509 4 2218083 1210459.8 0 2218083 5 219378 302614.9 0 219378 6 99427 75653.7 0 99427 7 69831 18913.4 0 69831 8 81144 4728.4 0 81144 9 69327 1182.1 0 65673 3654 10 86254 295.5 1 64771 21483 11 86689 73.9 1 66818 19871 12 152618 18.5 1 127131 25487 13 8000 4.6 1 4400 3600 14 142876 4.6 1 121534 21342 15 6164 4.6 1 3175 2989 16 157524 4.6 1 129484 28040 17 9368 4.6 1 5281 4087 18 110322 4.6 1 89737 20585 19 227175 4.6 1 198294 28881 20 2286 4.6 1 1173 1113 21 2562 4.6 1 970 1592 22 5827 4.6 1 2657 3170 23 88216 4.6 1 71209 17007 24 186505 4.6 1 158602 27903 25 8216 4.6 1 4608 3608 26 76802 4.6 1 61671 15131 27 65197 4.6 1 55637 9560 28 2895 4.6 1 1382 1513 29 67938 4.6 1 55476 12462 30 88509 4.6 1 73248 15261 31 107470 4.6 1 90166 17304 32 9768 4.6 1 5863 3905 33 124009 4.6 1 102313 21696 34 3169 4.6 1 1701 1468 35 65831 4.6 1 52431 13400 36 86774 4.6 1 70190 16584 37 100365 4.6 1 83307 17058 38 4565 4.6 1 2666 1899 39 79416 4.6 1 62736 16680 40 117161 4.6 1 92493 24668 41 6185 4.6 1 3649 2536 42 79241 4.6 1 60043 19198 43 98328 4.6 1 73247 25081 44 150109 4.6 1 119150 30959 45 31815 4.6 1 25768 6047 46 43480 4.6 1 31378 12102 47 4867 4.6 1 2963 1904 48 117730 4.6 1 95666 22064 49 64655 4.6 1 50519 14136 50 49998 4.6 1 37908 12090 51 80945 4.6 1 64124 16821 52 100481 4.6 1 82422 18059 53 35864 4.6 1 29124 6740 54 8281 4.6 1 5909 2372 55 114512 4.6 1 100445 14067 56 88023 4.6 1 74060 13963 57 9008 4.6 1 6800 2208 58 16584 4.6 1 11832 4752 59 79509 4.6 1 68186 11323 60 5679 4.6 1 3243 2436 61 13090 4.6 1 8529 4561 62 64280 4.6 1 54366 9914 63 3785 4.6 1 2002 1783 64 9323 4.6 1 5891 3432 65 22289 4.6 1 17071 5218 66 58348 4.6 1 49571 8777 67 27565 4.6 1 21718 5847 68 37093 4.6 1 30329 6764 69 29029 4.6 1 23079 5950 70 25492 4.6 1 19547 5945 71 12307 4.6 1 8398 3909 72 16100 4.6 1 12236 3864 73 24087 4.6 1 19483 4604 74 28372 4.6 1 23063 5309 75 30767 4.6 1 24926 5841 76 32489 4.6 1 26238 6251 77 32880 4.6 1 26516 6364 78 33544 4.6 1 26942 6602 79 33279 4.6 1 26423 6856 80 33181 4.6 1 26360 6821 81 33195 4.6 1 26291 6904 82 33217 4.6 1 26339 6878 83 32639 4.6 1 25624 7015 84 32054 4.6 1 25344 6710 85 31961 4.6 1 25110 6851 86 31461 4.6 1 24659 6802 87 31056 4.6 1 24375 6681 88 30928 4.6 1 24346 6582 89 29979 4.6 1 23608 6371 90 29702 4.6 1 23396 6306 91 29509 4.6 1 23084 6425 92 28807 4.6 1 22489 6318 93 27764 4.6 1 21767 5997 94 27551 4.6 1 21509 6042 95 26674 4.6 1 20797 5877 96 26566 4.6 1 20764 5802 97 25897 4.6 1 20320 5577 98 25130 4.6 1 19615 5515 99 24662 4.6 1 19241 5421 100 23805 4.6 1 18513 5292 101 23057 4.6 1 17989 5068 102 22484 4.6 1 17512 4972 103 22162 4.6 1 17259 4903 104 21057 4.6 1 16304 4753 105 20635 4.6 1 15939 4696 106 19695 4.6 1 15133 4562 107 18768 4.6 1 14393 4375 108 17844 4.6 1 13675 4169 109 17123 4.6 1 13124 3999 110 16499 4.6 1 12532 3967 111 15593 4.6 1 11916 3677 112 15113 4.6 1 11560 3553 113 14481 4.6 1 11021 3460 114 13889 4.6 1 10658 3231 115 13496 4.6 1 10426 3070 116 12857 4.6 1 9829 3028 117 12269 4.6 1 9412 2857 118 11754 4.6 1 8975 2779 119 11278 4.6 1 8643 2635 120 10276 4.6 1 7870 2406 121 10062 4.6 1 7696 2366 122 8939 4.6 1 6836 2103 123 8804 4.6 1 6816 1988 124 7987 4.6 1 6117 1870 125 7642 4.6 1 5918 1724 126 7156 4.6 1 5526 1630 127 6575 4.6 1 5123 1452 128 5937 4.6 1 4721 1216 129 6086 4.6 1 5006 1080 130 4836 4.6 1 3909 927 131 4800 4.6 1 4045 755 132 3687 4.6 1 3116 571 133 3273 4.6 1 2805 468 134 2904 4.6 1 2528 376 135 2541 4.6 1 2231 310 136 2071 4.6 1 1822 249 137 1835 4.6 1 1635 200 138 1525 4.6 1 1343 182 139 1248 4.6 1 1099 149 140 1075 4.6 1 952 123 141 817 4.6 1 727 90 142 833 4.6 1 735 98 143 705 4.6 1 627 78 144 566 4.6 1 506 60 145 527 4.6 1 448 79 146 584 4.6 1 496 88 147 490 4.6 1 431 59 148 592 4.6 1 486 106 149 548 4.6 1 429 119 150 899 4.6 1 543 356 151 72200 4.6 1 36351 35849 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz ============================================= 309877704 sequences processed in total