SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_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/NR015_AD015_S6_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 5993.33 s (24 us/read; 2.52 M reads/minute). === Summary === Total reads processed: 251,960,784 Reads with adapters: 98,150,549 (39.0%) Reads written (passing filters): 251,960,784 (100.0%) Total basepairs processed: 30,292,882,260 bp Quality-trimmed: 14,880,179 bp (0.0%) Total written (filtered): 29,870,391,799 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 98150549 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: 0.4% Overview of removed sequences length count expect max.err error counts 1 67647589 62990196.0 0 67647589 2 18152045 15747549.0 0 18152045 3 4775986 3936887.2 0 4775986 4 1890969 984221.8 0 1890969 5 207664 246055.5 0 207664 6 98537 61513.9 0 98537 7 74846 15378.5 0 74846 8 88166 3844.6 0 88166 9 80952 961.2 0 78131 2821 10 87335 240.3 1 73607 13728 11 89943 60.1 1 76934 13009 12 160853 15.0 1 146405 14448 13 4569 3.8 1 2624 1945 14 159804 3.8 1 145131 14673 15 3985 3.8 1 2223 1762 16 170314 3.8 1 151711 18603 17 7416 3.8 1 4591 2825 18 108590 3.8 1 97058 11532 19 256789 3.8 1 238071 18718 20 1865 3.8 1 1095 770 21 1505 3.8 1 703 802 22 3383 3.8 1 1937 1446 23 95821 3.8 1 85516 10305 24 198167 3.8 1 181758 16409 25 6239 3.8 1 4186 2053 26 75965 3.8 1 68109 7856 27 68321 3.8 1 63163 5158 28 2319 3.8 1 1409 910 29 72530 3.8 1 64801 7729 30 89129 3.8 1 80867 8262 31 111877 3.8 1 103485 8392 32 5769 3.8 1 4052 1717 33 127778 3.8 1 116285 11493 34 2818 3.8 1 1949 869 35 69936 3.8 1 61722 8214 36 66317 3.8 1 59395 6922 37 71065 3.8 1 64414 6651 38 107872 3.8 1 99240 8632 39 2490 3.8 1 1707 783 40 62577 3.8 1 55534 7043 41 60445 3.8 1 53846 6599 42 72395 3.8 1 63133 9262 43 79730 3.8 1 67556 12174 44 174322 3.8 1 155148 19174 45 33434 3.8 1 29737 3697 46 48312 3.8 1 40644 7668 47 8868 3.8 1 7169 1699 48 363712 3.8 1 346160 17552 49 159049 3.8 1 148984 10065 50 28469 3.8 1 24000 4469 51 87615 3.8 1 81660 5955 52 83971 3.8 1 77843 6128 53 16110 3.8 1 13174 2936 54 5077 3.8 1 3616 1461 55 40249 3.8 1 37342 2907 56 25311 3.8 1 22425 2886 57 4914 3.8 1 3521 1393 58 9531 3.8 1 7750 1781 59 15683 3.8 1 13352 2331 60 6108 3.8 1 4537 1571 61 9553 3.8 1 7756 1797 62 30625 3.8 1 28085 2540 63 6646 3.8 1 5279 1367 64 10476 3.8 1 8893 1583 65 12129 3.8 1 10311 1818 66 32496 3.8 1 30129 2367 67 9348 3.8 1 7566 1782 68 14758 3.8 1 12818 1940 69 17456 3.8 1 15424 2032 70 20192 3.8 1 18162 2030 71 8547 3.8 1 6817 1730 72 7395 3.8 1 5884 1511 73 13127 3.8 1 11639 1488 74 20669 3.8 1 18903 1766 75 24963 3.8 1 22902 2061 76 27047 3.8 1 24893 2154 77 27841 3.8 1 25567 2274 78 28052 3.8 1 25700 2352 79 28023 3.8 1 25545 2478 80 27896 3.8 1 25399 2497 81 27733 3.8 1 25291 2442 82 27390 3.8 1 24949 2441 83 26697 3.8 1 24265 2432 84 26722 3.8 1 24290 2432 85 25927 3.8 1 23433 2494 86 25310 3.8 1 22865 2445 87 25046 3.8 1 22605 2441 88 24529 3.8 1 22179 2350 89 24483 3.8 1 22077 2406 90 23988 3.8 1 21625 2363 91 22741 3.8 1 20617 2124 92 22201 3.8 1 20056 2145 93 21627 3.8 1 19471 2156 94 20771 3.8 1 18675 2096 95 20353 3.8 1 18316 2037 96 20197 3.8 1 18120 2077 97 19416 3.8 1 17499 1917 98 18926 3.8 1 17057 1869 99 18141 3.8 1 16272 1869 100 17620 3.8 1 15816 1804 101 17151 3.8 1 15427 1724 102 16211 3.8 1 14534 1677 103 15119 3.8 1 13497 1622 104 13828 3.8 1 12253 1575 105 12712 3.8 1 11213 1499 106 11640 3.8 1 10264 1376 107 10351 3.8 1 9001 1350 108 9064 3.8 1 7742 1322 109 8038 3.8 1 6793 1245 110 7411 3.8 1 6192 1219 111 6953 3.8 1 5785 1168 112 6592 3.8 1 5468 1124 113 6501 3.8 1 5458 1043 114 6362 3.8 1 5319 1043 115 6222 3.8 1 5249 973 116 5855 3.8 1 4900 955 117 6026 3.8 1 5076 950 118 5657 3.8 1 4820 837 119 5546 3.8 1 4708 838 120 5427 3.8 1 4637 790 121 5303 3.8 1 4551 752 122 4956 3.8 1 4286 670 123 5000 3.8 1 4290 710 124 4630 3.8 1 4031 599 125 5010 3.8 1 4393 617 126 4540 3.8 1 3960 580 127 4791 3.8 1 4274 517 128 4506 3.8 1 4038 468 129 7579 3.8 1 7009 570 130 4174 3.8 1 3794 380 131 6400 3.8 1 6002 398 132 4137 3.8 1 3882 255 133 4484 3.8 1 4219 265 134 3766 3.8 1 3564 202 135 4268 3.8 1 4046 222 136 3911 3.8 1 3717 194 137 4096 3.8 1 3915 181 138 3517 3.8 1 3375 142 139 3308 3.8 1 3157 151 140 3107 3.8 1 2996 111 141 3026 3.8 1 2901 125 142 2772 3.8 1 2650 122 143 3177 3.8 1 3054 123 144 2245 3.8 1 2121 124 145 2434 3.8 1 2302 132 146 2314 3.8 1 2195 119 147 2036 3.8 1 1898 138 148 1674 3.8 1 1487 187 149 1931 3.8 1 1679 252 150 4377 3.8 1 3025 1352 151 379957 3.8 1 180456 199501 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz ============================================= 251960784 sequences processed in total