SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.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/NR015_AD015_S6_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 6193.60 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 251,960,784 Reads with adapters: 100,979,622 (40.1%) Reads written (passing filters): 251,960,784 (100.0%) Total basepairs processed: 31,155,879,786 bp Quality-trimmed: 21,545,872 bp (0.1%) Total written (filtered): 30,661,317,524 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 100979622 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 23.0% G: 15.4% T: 29.6% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 68313199 62990196.0 0 68313199 2 18143166 15747549.0 0 18143166 3 5124109 3936887.2 0 5124109 4 1954723 984221.8 0 1954723 5 188739 246055.5 0 188739 6 129140 61513.9 0 129140 7 108832 15378.5 0 108832 8 128886 3844.6 0 128886 9 91260 961.2 0 87928 3332 10 126203 240.3 1 104830 21373 11 115077 60.1 1 96709 18368 12 226745 15.0 1 199323 27422 13 2194 3.8 1 959 1235 14 138238 3.8 1 118664 19574 15 191130 3.8 1 169718 21412 16 995 3.8 1 353 642 17 129094 3.8 1 113633 15461 18 79704 3.8 1 69960 9744 19 138252 3.8 1 121219 17033 20 100096 3.8 1 87894 12202 21 86564 3.8 1 75650 10914 22 101219 3.8 1 89374 11845 23 107692 3.8 1 94087 13605 24 189955 3.8 1 167177 22778 25 98024 3.8 1 87166 10858 26 98295 3.8 1 86572 11723 27 64815 3.8 1 54515 10300 28 155492 3.8 1 141126 14366 29 40546 3.8 1 32691 7855 30 146697 3.8 1 132730 13967 31 60422 3.8 1 51220 9202 32 268474 3.8 1 249368 19106 33 110795 3.8 1 97259 13536 34 38204 3.8 1 31226 6978 35 143638 3.8 1 131450 12188 36 47890 3.8 1 41399 6491 37 72520 3.8 1 63288 9232 38 37867 3.8 1 33785 4082 39 50949 3.8 1 44733 6216 40 20848 3.8 1 18228 2620 41 79085 3.8 1 71910 7175 42 111036 3.8 1 101963 9073 43 50564 3.8 1 44806 5758 44 82737 3.8 1 74481 8256 45 151990 3.8 1 139894 12096 46 71723 3.8 1 63298 8425 47 48816 3.8 1 44185 4631 48 148377 3.8 1 136657 11720 49 61498 3.8 1 55998 5500 50 23050 3.8 1 20044 3006 51 119426 3.8 1 109607 9819 52 183281 3.8 1 172910 10371 53 71389 3.8 1 66191 5198 54 89936 3.8 1 82844 7092 55 52537 3.8 1 48707 3830 56 25438 3.8 1 22287 3151 57 46738 3.8 1 42457 4281 58 50540 3.8 1 45618 4922 59 28544 3.8 1 25164 3380 60 18858 3.8 1 16100 2758 61 17190 3.8 1 14584 2606 62 18991 3.8 1 16327 2664 63 22581 3.8 1 19907 2674 64 38653 3.8 1 35535 3118 65 48769 3.8 1 44750 4019 66 52547 3.8 1 48219 4328 67 52683 3.8 1 48131 4552 68 52201 3.8 1 47603 4598 69 52101 3.8 1 47443 4658 70 51853 3.8 1 47277 4576 71 51340 3.8 1 46653 4687 72 50223 3.8 1 45673 4550 73 49914 3.8 1 45383 4531 74 48369 3.8 1 43891 4478 75 47815 3.8 1 43411 4404 76 46803 3.8 1 42428 4375 77 46237 3.8 1 42021 4216 78 44826 3.8 1 40634 4192 79 43489 3.8 1 39420 4069 80 43261 3.8 1 39363 3898 81 42442 3.8 1 38480 3962 82 41492 3.8 1 37628 3864 83 40374 3.8 1 36728 3646 84 39695 3.8 1 36017 3678 85 39208 3.8 1 35580 3628 86 38171 3.8 1 34599 3572 87 38016 3.8 1 34553 3463 88 36525 3.8 1 33092 3433 89 41258 3.8 1 33003 8255 90 34752 3.8 1 31007 3745 91 33218 3.8 1 30100 3118 92 32601 3.8 1 29475 3126 93 31952 3.8 1 28947 3005 94 31006 3.8 1 28057 2949 95 30263 3.8 1 27427 2836 96 29561 3.8 1 26776 2785 97 28672 3.8 1 25981 2691 98 27549 3.8 1 24930 2619 99 26632 3.8 1 24067 2565 100 25886 3.8 1 23427 2459 101 24490 3.8 1 22115 2375 102 23311 3.8 1 21015 2296 103 21482 3.8 1 19313 2169 104 19671 3.8 1 17609 2062 105 17882 3.8 1 15906 1976 106 15683 3.8 1 13909 1774 107 13366 3.8 1 11584 1782 108 11524 3.8 1 9775 1749 109 9805 3.8 1 8171 1634 110 8591 3.8 1 7096 1495 111 8086 3.8 1 6610 1476 112 7566 3.8 1 6240 1326 113 7509 3.8 1 6118 1391 114 7162 3.8 1 5878 1284 115 7027 3.8 1 5812 1215 116 6711 3.8 1 5506 1205 117 6602 3.8 1 5438 1164 118 6295 3.8 1 5252 1043 119 6307 3.8 1 5204 1103 120 6026 3.8 1 5073 953 121 5936 3.8 1 5017 919 122 5503 3.8 1 4654 849 123 5535 3.8 1 4715 820 124 5175 3.8 1 4422 753 125 5396 3.8 1 4729 667 126 5052 3.8 1 4370 682 127 5194 3.8 1 4586 608 128 4771 3.8 1 4258 513 129 7872 3.8 1 7315 557 130 4352 3.8 1 3923 429 131 6565 3.8 1 6168 397 132 4192 3.8 1 3862 330 133 4550 3.8 1 4240 310 134 3843 3.8 1 3560 283 135 4287 3.8 1 4041 246 136 3693 3.8 1 3402 291 137 4048 3.8 1 3789 259 138 3506 3.8 1 3254 252 139 3304 3.8 1 3036 268 140 3120 3.8 1 2843 277 141 3010 3.8 1 2684 326 142 2563 3.8 1 2214 349 143 2946 3.8 1 2557 389 144 2247 3.8 1 1857 390 145 2380 3.8 1 1931 449 146 1903 3.8 1 1439 464 147 1848 3.8 1 1414 434 148 1435 3.8 1 985 450 149 1587 3.8 1 1131 456 150 3495 3.8 1 2865 630 151 169848 3.8 1 165158 4690 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz ============================================= 251960784 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 251960784 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1195829 (0.47%)