SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_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/AD002_S9_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 4009.23 s (24 us/read; 2.49 M reads/minute). === Summary === Total reads processed: 166,519,549 Reads with adapters: 62,950,909 (37.8%) Reads written (passing filters): 166,519,549 (100.0%) Total basepairs processed: 20,263,772,384 bp Quality-trimmed: 10,658,407 bp (0.1%) Total written (filtered): 20,075,819,474 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62950909 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 22.7% G: 14.4% T: 30.1% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 45191016 41629887.2 0 45191016 2 11892878 10407471.8 0 11892878 3 3014795 2601868.0 0 3014795 4 1184885 650467.0 0 1184885 5 136203 162616.7 0 136203 6 26162 40654.2 0 26162 7 15017 10163.5 0 15017 8 16951 2540.9 0 16951 9 13393 635.2 0 11409 1984 10 20526 158.8 1 12168 8358 11 18484 39.7 1 12657 5827 12 30871 9.9 1 23904 6967 13 1883 2.5 1 977 906 14 28295 2.5 1 22411 5884 15 1728 2.5 1 845 883 16 31609 2.5 1 24109 7500 17 2352 2.5 1 1197 1155 18 22811 2.5 1 17377 5434 19 44221 2.5 1 36321 7900 20 476 2.5 1 204 272 21 735 2.5 1 260 475 22 1509 2.5 1 663 846 23 19790 2.5 1 14697 5093 24 38449 2.5 1 30670 7779 25 2192 2.5 1 1125 1067 26 16807 2.5 1 12495 4312 27 13827 2.5 1 11153 2674 28 810 2.5 1 317 493 29 16333 2.5 1 12128 4205 30 20883 2.5 1 16077 4806 31 24181 2.5 1 19042 5139 32 3089 2.5 1 1832 1257 33 29110 2.5 1 22048 7062 34 14162 2.5 1 11204 2958 35 817 2.5 1 349 468 36 16927 2.5 1 12775 4152 37 19935 2.5 1 15059 4876 38 12063 2.5 1 8977 3086 39 18055 2.5 1 13767 4288 40 16204 2.5 1 12318 3886 41 19447 2.5 1 14427 5020 42 35132 2.5 1 27593 7539 43 6650 2.5 1 5421 1229 44 9775 2.5 1 6973 2802 45 796 2.5 1 368 428 46 19159 2.5 1 14642 4517 47 14576 2.5 1 11098 3478 48 13926 2.5 1 10450 3476 49 19134 2.5 1 13988 5146 50 29774 2.5 1 23411 6363 51 10816 2.5 1 8626 2190 52 2049 2.5 1 1278 771 53 28745 2.5 1 22950 5795 54 35400 2.5 1 28635 6765 55 3293 2.5 1 2440 853 56 8907 2.5 1 6800 2107 57 29998 2.5 1 24644 5354 58 1367 2.5 1 744 623 59 3980 2.5 1 2473 1507 60 25914 2.5 1 21592 4322 61 732 2.5 1 362 370 62 2084 2.5 1 1131 953 63 7543 2.5 1 5611 1932 64 19408 2.5 1 15793 3615 65 16686 2.5 1 13541 3145 66 16846 2.5 1 13865 2981 67 9203 2.5 1 7168 2035 68 7795 2.5 1 5744 2051 69 5135 2.5 1 3682 1453 70 5891 2.5 1 4597 1294 71 8634 2.5 1 6924 1710 72 9794 2.5 1 7862 1932 73 10352 2.5 1 8360 1992 74 10759 2.5 1 8560 2199 75 11037 2.5 1 8815 2222 76 11355 2.5 1 9027 2328 77 11168 2.5 1 8869 2299 78 11167 2.5 1 8809 2358 79 11221 2.5 1 8924 2297 80 11098 2.5 1 8767 2331 81 10888 2.5 1 8548 2340 82 10994 2.5 1 8677 2317 83 10736 2.5 1 8441 2295 84 10842 2.5 1 8489 2353 85 10728 2.5 1 8418 2310 86 10495 2.5 1 8215 2280 87 10484 2.5 1 8225 2259 88 10007 2.5 1 7802 2205 89 10091 2.5 1 7857 2234 90 9940 2.5 1 7828 2112 91 9628 2.5 1 7583 2045 92 9575 2.5 1 7475 2100 93 9431 2.5 1 7431 2000 94 9329 2.5 1 7319 2010 95 8980 2.5 1 6971 2009 96 8950 2.5 1 7007 1943 97 8734 2.5 1 6774 1960 98 8538 2.5 1 6692 1846 99 8250 2.5 1 6355 1895 100 8216 2.5 1 6456 1760 101 7764 2.5 1 6063 1701 102 7618 2.5 1 5928 1690 103 7234 2.5 1 5651 1583 104 6971 2.5 1 5450 1521 105 6699 2.5 1 5123 1576 106 6627 2.5 1 5073 1554 107 6023 2.5 1 4625 1398 108 5843 2.5 1 4473 1370 109 5608 2.5 1 4271 1337 110 5329 2.5 1 4030 1299 111 5128 2.5 1 3929 1199 112 4870 2.5 1 3694 1176 113 4622 2.5 1 3450 1172 114 4528 2.5 1 3397 1131 115 4255 2.5 1 3226 1029 116 4100 2.5 1 3085 1015 117 3886 2.5 1 2902 984 118 3780 2.5 1 2870 910 119 3676 2.5 1 2785 891 120 3372 2.5 1 2520 852 121 3199 2.5 1 2440 759 122 2979 2.5 1 2269 710 123 2811 2.5 1 2107 704 124 2615 2.5 1 1971 644 125 2537 2.5 1 1908 629 126 2335 2.5 1 1795 540 127 2138 2.5 1 1639 499 128 2019 2.5 1 1567 452 129 1900 2.5 1 1514 386 130 1584 2.5 1 1268 316 131 1574 2.5 1 1292 282 132 1236 2.5 1 1037 199 133 1139 2.5 1 979 160 134 950 2.5 1 804 146 135 914 2.5 1 788 126 136 764 2.5 1 646 118 137 685 2.5 1 601 84 138 556 2.5 1 487 69 139 495 2.5 1 442 53 140 421 2.5 1 358 63 141 343 2.5 1 295 48 142 266 2.5 1 225 41 143 305 2.5 1 243 62 144 238 2.5 1 195 43 145 269 2.5 1 214 55 146 219 2.5 1 174 45 147 245 2.5 1 185 60 148 203 2.5 1 128 75 149 310 2.5 1 192 118 150 1172 2.5 1 461 711 151 114539 2.5 1 42001 72538 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz ============================================= 166519549 sequences processed in total