SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck --threads 28 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.14 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 10716.32 s (28 us/read; 2.11 M reads/minute). === Summary === Total reads processed: 377,720,238 Reads with adapters: 81,190,946 (21.5%) Reads written (passing filters): 377,720,238 (100.0%) Total basepairs processed: 44,137,321,483 bp Quality-trimmed: 1,790,708,809 bp (4.1%) Total written (filtered): 42,153,855,184 bp (95.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 81190946 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 23.2% G: 14.3% T: 29.4% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 60062944 94430059.5 0 60062944 2 14458552 23607514.9 0 14458552 3 3668644 5901878.7 0 3668644 4 1514088 1475469.7 0 1514088 5 296428 368867.4 0 296428 6 34325 92216.9 0 34325 7 17506 23054.2 0 17506 8 11030 5763.6 0 11030 9 2952 1440.9 0 847 2105 10 12326 360.2 1 4426 7900 11 2746 90.1 1 570 2176 12 5760 22.5 1 3870 1890 13 6237 5.6 1 4374 1863 14 4689 5.6 1 3488 1201 15 5952 5.6 1 4256 1696 16 4675 5.6 1 3479 1196 17 2519 5.6 1 1132 1387 18 9156 5.6 1 6359 2797 19 14052 5.6 1 11787 2265 20 1959 5.6 1 934 1025 21 1367 5.6 1 621 746 22 7274 5.6 1 5216 2058 23 5488 5.6 1 4117 1371 24 7754 5.6 1 6325 1429 25 2859 5.6 1 1654 1205 26 4354 5.6 1 3345 1009 27 5628 5.6 1 4243 1385 28 10234 5.6 1 7980 2254 29 1344 5.6 1 660 684 30 4079 5.6 1 2740 1339 31 6952 5.6 1 5654 1298 32 6107 5.6 1 4595 1512 33 4687 5.6 1 3686 1001 34 6836 5.6 1 5001 1835 35 3195 5.6 1 1882 1313 36 5117 5.6 1 3952 1165 37 7224 5.6 1 5495 1729 38 8831 5.6 1 7254 1577 39 14332 5.6 1 11919 2413 40 1625 5.6 1 891 734 41 4743 5.6 1 3149 1594 42 6951 5.6 1 5435 1516 43 8013 5.6 1 6814 1199 44 5498 5.6 1 4328 1170 45 1442 5.6 1 828 614 46 4060 5.6 1 3291 769 47 1578 5.6 1 940 638 48 6955 5.6 1 5512 1443 49 8571 5.6 1 7255 1316 50 1772 5.6 1 1103 669 51 5242 5.6 1 4253 989 52 9256 5.6 1 7778 1478 53 6058 5.6 1 4864 1194 54 3057 5.6 1 2080 977 55 12152 5.6 1 10091 2061 56 8887 5.6 1 7741 1146 57 3891 5.6 1 2845 1046 58 3771 5.6 1 2944 827 59 12626 5.6 1 11334 1292 60 1864 5.6 1 1200 664 61 1479 5.6 1 998 481 62 8820 5.6 1 7630 1190 63 3154 5.6 1 2248 906 64 2696 5.6 1 1965 731 65 5457 5.6 1 4557 900 66 12512 5.6 1 10804 1708 67 5927 5.6 1 5025 902 68 5574 5.6 1 4706 868 69 6120 5.6 1 5206 914 70 6130 5.6 1 5187 943 71 6553 5.6 1 5494 1059 72 7316 5.6 1 6051 1265 73 8909 5.6 1 7176 1733 74 12845 5.6 1 8768 4077 75 75976 5.6 1 15028 60948 76 148428 5.6 1 102903 45525 77 107146 5.6 1 78133 29013 78 62019 5.6 1 42416 19603 79 36095 5.6 1 25235 10860 80 22919 5.6 1 15603 7316 81 14348 5.6 1 9634 4714 82 9658 5.6 1 6469 3189 83 7234 5.6 1 4728 2506 84 5798 5.6 1 3768 2030 85 5156 5.6 1 3393 1763 86 4721 5.6 1 3064 1657 87 4576 5.6 1 3054 1522 88 4309 5.6 1 2961 1348 89 4336 5.6 1 3032 1304 90 3815 5.6 1 2568 1247 91 3683 5.6 1 2482 1201 92 3520 5.6 1 2365 1155 93 3172 5.6 1 2169 1003 94 3230 5.6 1 2262 968 95 3028 5.6 1 2090 938 96 3172 5.6 1 2185 987 97 2839 5.6 1 1950 889 98 2858 5.6 1 2041 817 99 2924 5.6 1 2091 833 100 2721 5.6 1 1899 822 101 2683 5.6 1 1927 756 102 2660 5.6 1 1845 815 103 2498 5.6 1 1795 703 104 2571 5.6 1 1853 718 105 2510 5.6 1 1801 709 106 2381 5.6 1 1731 650 107 2401 5.6 1 1713 688 108 2365 5.6 1 1680 685 109 2297 5.6 1 1682 615 110 2280 5.6 1 1660 620 111 2167 5.6 1 1609 558 112 2135 5.6 1 1521 614 113 2021 5.6 1 1450 571 114 2007 5.6 1 1436 571 115 1964 5.6 1 1412 552 116 1975 5.6 1 1444 531 117 1951 5.6 1 1444 507 118 1938 5.6 1 1458 480 119 1810 5.6 1 1396 414 120 1871 5.6 1 1375 496 121 1697 5.6 1 1274 423 122 1702 5.6 1 1288 414 123 1604 5.6 1 1174 430 124 1678 5.6 1 1262 416 125 1610 5.6 1 1242 368 126 1620 5.6 1 1245 375 127 1580 5.6 1 1200 380 128 1859 5.6 1 1522 337 129 1599 5.6 1 1292 307 130 1553 5.6 1 1260 293 131 1494 5.6 1 1217 277 132 1329 5.6 1 1040 289 133 1335 5.6 1 1054 281 134 1416 5.6 1 1103 313 135 1423 5.6 1 1081 342 136 1703 5.6 1 1316 387 137 2071 5.6 1 1630 441 138 5334 5.6 1 4925 409 139 3326 5.6 1 2967 359 140 2196 5.6 1 1826 370 141 1596 5.6 1 1245 351 142 1408 5.6 1 986 422 143 1380 5.6 1 908 472 144 1473 5.6 1 953 520 145 1520 5.6 1 897 623 146 1854 5.6 1 967 887 147 2646 5.6 1 1293 1353 148 5516 5.6 1 2385 3131 149 13966 5.6 1 6048 7918 150 47659 5.6 1 20533 27126 151 19927 5.6 1 7446 12481 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001.fastq.gz ============================================= 377720238 sequences processed in total