SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_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/NR015_AD015_S6_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 6925.44 s (24 us/read; 2.48 M reads/minute). === Summary === Total reads processed: 286,345,514 Reads with adapters: 112,959,695 (39.4%) Reads written (passing filters): 286,345,514 (100.0%) Total basepairs processed: 35,038,018,789 bp Quality-trimmed: 13,805,282 bp (0.0%) Total written (filtered): 34,518,982,225 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 112959695 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.6% C: 23.5% G: 14.7% T: 29.7% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 78396135 71586378.5 0 78396135 2 20488392 17896594.6 0 20488392 3 5379582 4474148.7 0 5379582 4 2080584 1118537.2 0 2080584 5 223491 279634.3 0 223491 6 100154 69908.6 0 100154 7 75732 17477.1 0 75732 8 86633 4369.3 0 86633 9 80998 1092.3 0 77642 3356 10 88682 273.1 1 74287 14395 11 90629 68.3 1 77841 12788 12 161905 17.1 1 148361 13544 13 4301 4.3 1 2285 2016 14 160121 4.3 1 146934 13187 15 3804 4.3 1 1935 1869 16 171383 4.3 1 153699 17684 17 7255 4.3 1 4345 2910 18 107431 4.3 1 96486 10945 19 265068 4.3 1 247099 17969 20 1979 4.3 1 1118 861 21 1742 4.3 1 801 941 22 3763 4.3 1 2101 1662 23 95718 4.3 1 85159 10559 24 206250 4.3 1 190203 16047 25 6546 4.3 1 4203 2343 26 78594 4.3 1 70732 7862 27 70370 4.3 1 65520 4850 28 2519 4.3 1 1512 1007 29 75709 4.3 1 67862 7847 30 91570 4.3 1 83304 8266 31 117793 4.3 1 109087 8706 32 6339 4.3 1 4304 2035 33 137342 4.3 1 124884 12458 34 3254 4.3 1 2205 1049 35 75697 4.3 1 66263 9434 36 70974 4.3 1 63418 7556 37 76030 4.3 1 68817 7213 38 118275 4.3 1 108426 9849 39 2841 4.3 1 1941 900 40 69529 4.3 1 61210 8319 41 68776 4.3 1 60720 8056 42 82760 4.3 1 70525 12235 43 94151 4.3 1 77798 16353 44 204930 4.3 1 180380 24550 45 38013 4.3 1 33457 4556 46 54282 4.3 1 44999 9283 47 11755 4.3 1 9625 2130 48 492920 4.3 1 471229 21691 49 144283 4.3 1 132748 11535 50 29210 4.3 1 23840 5370 51 111750 4.3 1 103977 7773 52 84336 4.3 1 76899 7437 53 14904 4.3 1 11273 3631 54 6028 4.3 1 4207 1821 55 38270 4.3 1 34920 3350 56 20143 4.3 1 16575 3568 57 4741 4.3 1 3048 1693 58 9097 4.3 1 6744 2353 59 20031 4.3 1 17035 2996 60 6411 4.3 1 4486 1925 61 9287 4.3 1 6932 2355 62 31197 4.3 1 28051 3146 63 5622 4.3 1 4034 1588 64 9211 4.3 1 7161 2050 65 14746 4.3 1 12258 2488 66 33048 4.3 1 29926 3122 67 11214 4.3 1 8789 2425 68 24371 4.3 1 21564 2807 69 30605 4.3 1 27502 3103 70 44875 4.3 1 41184 3691 71 17999 4.3 1 15248 2751 72 8543 4.3 1 6252 2291 73 12632 4.3 1 10441 2191 74 22706 4.3 1 20346 2360 75 30225 4.3 1 27494 2731 76 33537 4.3 1 30537 3000 77 35713 4.3 1 32516 3197 78 36158 4.3 1 32668 3490 79 36710 4.3 1 33136 3574 80 36902 4.3 1 33217 3685 81 36541 4.3 1 32897 3644 82 36501 4.3 1 32621 3880 83 35623 4.3 1 31806 3817 84 35658 4.3 1 31851 3807 85 35471 4.3 1 31655 3816 86 34536 4.3 1 30760 3776 87 33782 4.3 1 30227 3555 88 33922 4.3 1 30047 3875 89 33565 4.3 1 29789 3776 90 33858 4.3 1 30148 3710 91 32373 4.3 1 28635 3738 92 31605 4.3 1 28042 3563 93 30634 4.3 1 27154 3480 94 30011 4.3 1 26517 3494 95 29452 4.3 1 25995 3457 96 29070 4.3 1 25623 3447 97 28471 4.3 1 25113 3358 98 27941 4.3 1 24728 3213 99 27386 4.3 1 24187 3199 100 26522 4.3 1 23386 3136 101 25249 4.3 1 22180 3069 102 24525 4.3 1 21350 3175 103 23581 4.3 1 20579 3002 104 22163 4.3 1 19173 2990 105 20739 4.3 1 17886 2853 106 19555 4.3 1 16798 2757 107 17970 4.3 1 15280 2690 108 16213 4.3 1 13719 2494 109 14971 4.3 1 12491 2480 110 14369 4.3 1 11949 2420 111 13676 4.3 1 11409 2267 112 13279 4.3 1 10889 2390 113 12986 4.3 1 10823 2163 114 12529 4.3 1 10316 2213 115 12359 4.3 1 10273 2086 116 11824 4.3 1 9721 2103 117 11521 4.3 1 9680 1841 118 11341 4.3 1 9443 1898 119 10814 4.3 1 9101 1713 120 10536 4.3 1 8822 1714 121 10223 4.3 1 8608 1615 122 9654 4.3 1 8123 1531 123 9335 4.3 1 7885 1450 124 8797 4.3 1 7489 1308 125 8983 4.3 1 7661 1322 126 8427 4.3 1 7191 1236 127 8872 4.3 1 7688 1184 128 7881 4.3 1 6883 998 129 11912 4.3 1 10868 1044 130 7024 4.3 1 6278 746 131 10003 4.3 1 9240 763 132 6500 4.3 1 5991 509 133 6890 4.3 1 6514 376 134 5695 4.3 1 5351 344 135 6358 4.3 1 6012 346 136 5449 4.3 1 5171 278 137 5778 4.3 1 5554 224 138 4758 4.3 1 4570 188 139 4546 4.3 1 4383 163 140 4169 4.3 1 3998 171 141 3895 4.3 1 3759 136 142 3337 4.3 1 3215 122 143 3888 4.3 1 3761 127 144 3019 4.3 1 2893 126 145 3195 4.3 1 3069 126 146 2750 4.3 1 2613 137 147 2411 4.3 1 2277 134 148 1979 4.3 1 1816 163 149 2200 4.3 1 2002 198 150 3790 4.3 1 2743 1047 151 507649 4.3 1 240906 266743 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz ============================================= 286345514 sequences processed in total