SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-1_S1_L001_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-1_S1_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 11276.36 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 368,469,262 Reads with adapters: 79,594,596 (21.6%) Reads written (passing filters): 368,469,262 (100.0%) Total basepairs processed: 44,653,718,483 bp Quality-trimmed: 1,544,810,377 bp (3.5%) Total written (filtered): 42,952,779,623 bp (96.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 79594596 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.4% C: 22.3% G: 13.9% T: 29.3% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 60105325 92117315.5 0 60105325 2 13304644 23029328.9 0 13304644 3 3563395 5757332.2 0 3563395 4 1494825 1439333.1 0 1494825 5 284071 359833.3 0 284071 6 34958 89958.3 0 34958 7 18635 22489.6 0 18635 8 9808 5622.4 0 9808 9 3174 1405.6 0 1075 2099 10 12903 351.4 1 4177 8726 11 3209 87.8 1 721 2488 12 6310 22.0 1 3722 2588 13 7013 5.5 1 4292 2721 14 4967 5.5 1 3207 1760 15 6446 5.5 1 4002 2444 16 5136 5.5 1 3293 1843 17 3315 5.5 1 1500 1815 18 11099 5.5 1 7038 4061 19 12966 5.5 1 9723 3243 20 2029 5.5 1 852 1177 21 1735 5.5 1 724 1011 22 7984 5.5 1 5026 2958 23 5421 5.5 1 3516 1905 24 8278 5.5 1 6009 2269 25 3185 5.5 1 1582 1603 26 5173 5.5 1 3430 1743 27 6047 5.5 1 3980 2067 28 11376 5.5 1 7753 3623 29 2049 5.5 1 936 1113 30 4589 5.5 1 2764 1825 31 6916 5.5 1 5020 1896 32 6246 5.5 1 4221 2025 33 5580 5.5 1 3803 1777 34 6925 5.5 1 4486 2439 35 5226 5.5 1 2710 2516 36 17183 5.5 1 11702 5481 37 6390 5.5 1 4056 2334 38 3701 5.5 1 2470 1231 39 9744 5.5 1 6961 2783 40 8291 5.5 1 5970 2321 41 6421 5.5 1 4838 1583 42 6431 5.5 1 4351 2080 43 2171 5.5 1 1148 1023 44 4000 5.5 1 2771 1229 45 1994 5.5 1 1042 952 46 8102 5.5 1 5687 2415 47 8569 5.5 1 6379 2190 48 2457 5.5 1 1418 1039 49 5387 5.5 1 3816 1571 50 9522 5.5 1 7173 2349 51 6717 5.5 1 4823 1894 52 3854 5.5 1 2274 1580 53 14118 5.5 1 10703 3415 54 8290 5.5 1 6302 1988 55 5163 5.5 1 3556 1607 56 4759 5.5 1 3321 1438 57 11331 5.5 1 9048 2283 58 2678 5.5 1 1617 1061 59 1823 5.5 1 1028 795 60 9101 5.5 1 7066 2035 61 4342 5.5 1 2831 1511 62 3666 5.5 1 2479 1187 63 5505 5.5 1 4049 1456 64 13068 5.5 1 10103 2965 65 6346 5.5 1 4737 1609 66 5739 5.5 1 4383 1356 67 6105 5.5 1 4632 1473 68 6135 5.5 1 4660 1475 69 6534 5.5 1 4979 1555 70 6979 5.5 1 5288 1691 71 7559 5.5 1 5857 1702 72 8738 5.5 1 6491 2247 73 38520 5.5 1 8918 29602 74 60833 5.5 1 37982 22851 75 32033 5.5 1 21254 10779 76 16561 5.5 1 10168 6393 77 11258 5.5 1 6829 4429 78 8014 5.5 1 4889 3125 79 6569 5.5 1 3986 2583 80 5625 5.5 1 3520 2105 81 5058 5.5 1 3212 1846 82 4996 5.5 1 3190 1806 83 4794 5.5 1 3036 1758 84 4788 5.5 1 3074 1714 85 4600 5.5 1 2944 1656 86 4341 5.5 1 2830 1511 87 4435 5.5 1 2902 1533 88 4424 5.5 1 2924 1500 89 4240 5.5 1 2758 1482 90 4046 5.5 1 2650 1396 91 4137 5.5 1 2729 1408 92 3844 5.5 1 2517 1327 93 3829 5.5 1 2555 1274 94 3727 5.5 1 2391 1336 95 3800 5.5 1 2500 1300 96 3504 5.5 1 2317 1187 97 3489 5.5 1 2346 1143 98 3480 5.5 1 2346 1134 99 3457 5.5 1 2343 1114 100 3254 5.5 1 2254 1000 101 3294 5.5 1 2219 1075 102 3057 5.5 1 2023 1034 103 3008 5.5 1 2042 966 104 2858 5.5 1 1916 942 105 2823 5.5 1 1928 895 106 2796 5.5 1 1864 932 107 2761 5.5 1 1864 897 108 2755 5.5 1 1836 919 109 2537 5.5 1 1741 796 110 2486 5.5 1 1682 804 111 2380 5.5 1 1573 807 112 2432 5.5 1 1690 742 113 2207 5.5 1 1481 726 114 2128 5.5 1 1408 720 115 2078 5.5 1 1403 675 116 1982 5.5 1 1320 662 117 1875 5.5 1 1244 631 118 1759 5.5 1 1247 512 119 1678 5.5 1 1120 558 120 1655 5.5 1 1152 503 121 1587 5.5 1 1074 513 122 1441 5.5 1 948 493 123 1379 5.5 1 911 468 124 1259 5.5 1 823 436 125 1267 5.5 1 836 431 126 1167 5.5 1 784 383 127 991 5.5 1 676 315 128 887 5.5 1 616 271 129 737 5.5 1 506 231 130 667 5.5 1 455 212 131 580 5.5 1 389 191 132 526 5.5 1 333 193 133 519 5.5 1 344 175 134 494 5.5 1 321 173 135 397 5.5 1 232 165 136 395 5.5 1 202 193 137 387 5.5 1 198 189 138 360 5.5 1 209 151 139 304 5.5 1 126 178 140 338 5.5 1 131 207 141 371 5.5 1 147 224 142 358 5.5 1 139 219 143 407 5.5 1 132 275 144 411 5.5 1 162 249 145 549 5.5 1 173 376 146 694 5.5 1 227 467 147 1002 5.5 1 281 721 148 2028 5.5 1 631 1397 149 5434 5.5 1 1650 3784 150 17673 5.5 1 5166 12507 151 9911 5.5 1 2839 7072 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-1_S1_L001_R1_001.fastq.gz ============================================= 368469262 sequences processed in total