SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_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-7_S28_L007_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 10626.56 s (29 us/read; 2.10 M reads/minute). === Summary === Total reads processed: 372,443,998 Reads with adapters: 80,265,508 (21.6%) Reads written (passing filters): 372,443,998 (100.0%) Total basepairs processed: 43,423,870,063 bp Quality-trimmed: 1,813,021,197 bp (4.2%) Total written (filtered): 41,416,634,105 bp (95.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80265508 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.5% C: 23.3% G: 14.3% T: 29.4% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 59245360 93110999.5 0 59245360 2 14414406 23277749.9 0 14414406 3 3607115 5819437.5 0 3607115 4 1486890 1454859.4 0 1486890 5 289552 363714.8 0 289552 6 33411 90928.7 0 33411 7 17904 22732.2 0 17904 8 11002 5683.0 0 11002 9 3111 1420.8 0 904 2207 10 12404 355.2 1 4357 8047 11 2688 88.8 1 584 2104 12 5889 22.2 1 3925 1964 13 6122 5.5 1 4224 1898 14 4855 5.5 1 3576 1279 15 5909 5.5 1 4188 1721 16 4703 5.5 1 3482 1221 17 2831 5.5 1 1321 1510 18 9730 5.5 1 6763 2967 19 14222 5.5 1 11869 2353 20 2075 5.5 1 953 1122 21 1359 5.5 1 628 731 22 7466 5.5 1 5236 2230 23 5444 5.5 1 4059 1385 24 7650 5.5 1 6192 1458 25 3013 5.5 1 1781 1232 26 4510 5.5 1 3425 1085 27 5655 5.5 1 4257 1398 28 10377 5.5 1 8042 2335 29 1449 5.5 1 697 752 30 4372 5.5 1 2965 1407 31 6837 5.5 1 5631 1206 32 6183 5.5 1 4701 1482 33 4569 5.5 1 3638 931 34 6898 5.5 1 5030 1868 35 3456 5.5 1 2090 1366 36 5169 5.5 1 3995 1174 37 7375 5.5 1 5624 1751 38 8775 5.5 1 7203 1572 39 14454 5.5 1 11975 2479 40 1694 5.5 1 942 752 41 5066 5.5 1 3330 1736 42 7061 5.5 1 5536 1525 43 8462 5.5 1 7229 1233 44 5510 5.5 1 4365 1145 45 1514 5.5 1 881 633 46 4120 5.5 1 3375 745 47 1717 5.5 1 1046 671 48 7121 5.5 1 5708 1413 49 8480 5.5 1 7212 1268 50 1906 5.5 1 1200 706 51 5223 5.5 1 4238 985 52 9373 5.5 1 7946 1427 53 6325 5.5 1 5052 1273 54 3170 5.5 1 2117 1053 55 12433 5.5 1 10395 2038 56 9115 5.5 1 7913 1202 57 4068 5.5 1 2942 1126 58 3976 5.5 1 3100 876 59 12760 5.5 1 11575 1185 60 1943 5.5 1 1320 623 61 1528 5.5 1 991 537 62 8979 5.5 1 7799 1180 63 3476 5.5 1 2480 996 64 2768 5.5 1 2016 752 65 5589 5.5 1 4669 920 66 13129 5.5 1 11342 1787 67 6377 5.5 1 5448 929 68 5667 5.5 1 4789 878 69 6342 5.5 1 5412 930 70 6305 5.5 1 5389 916 71 6755 5.5 1 5725 1030 72 7787 5.5 1 6493 1294 73 8902 5.5 1 7237 1665 74 13116 5.5 1 9011 4105 75 68811 5.5 1 14808 54003 76 141022 5.5 1 94577 46445 77 110493 5.5 1 78201 32292 78 70912 5.5 1 47609 23303 79 43363 5.5 1 29584 13779 80 26403 5.5 1 17825 8578 81 16565 5.5 1 11018 5547 82 11322 5.5 1 7432 3890 83 8285 5.5 1 5361 2924 84 6571 5.5 1 4277 2294 85 5574 5.5 1 3633 1941 86 5068 5.5 1 3272 1796 87 4931 5.5 1 3334 1597 88 4592 5.5 1 3129 1463 89 4595 5.5 1 3167 1428 90 4076 5.5 1 2733 1343 91 3751 5.5 1 2520 1231 92 3593 5.5 1 2447 1146 93 3468 5.5 1 2391 1077 94 3295 5.5 1 2277 1018 95 3329 5.5 1 2277 1052 96 3110 5.5 1 2133 977 97 3148 5.5 1 2148 1000 98 3016 5.5 1 2104 912 99 2946 5.5 1 2071 875 100 2902 5.5 1 2040 862 101 2885 5.5 1 2039 846 102 2707 5.5 1 1910 797 103 2561 5.5 1 1848 713 104 2526 5.5 1 1740 786 105 2620 5.5 1 1896 724 106 2561 5.5 1 1839 722 107 2359 5.5 1 1730 629 108 2459 5.5 1 1800 659 109 2312 5.5 1 1652 660 110 2253 5.5 1 1656 597 111 2215 5.5 1 1618 597 112 2163 5.5 1 1545 618 113 2085 5.5 1 1507 578 114 2158 5.5 1 1590 568 115 2005 5.5 1 1479 526 116 2107 5.5 1 1563 544 117 2052 5.5 1 1532 520 118 2039 5.5 1 1512 527 119 2019 5.5 1 1493 526 120 1942 5.5 1 1475 467 121 1812 5.5 1 1316 496 122 1801 5.5 1 1333 468 123 1736 5.5 1 1305 431 124 1729 5.5 1 1296 433 125 1708 5.5 1 1318 390 126 1689 5.5 1 1314 375 127 1622 5.5 1 1257 365 128 1974 5.5 1 1601 373 129 1616 5.5 1 1294 322 130 1692 5.5 1 1347 345 131 1542 5.5 1 1212 330 132 1467 5.5 1 1163 304 133 1390 5.5 1 1074 316 134 1418 5.5 1 1108 310 135 1543 5.5 1 1163 380 136 1710 5.5 1 1306 404 137 2114 5.5 1 1668 446 138 5226 5.5 1 4790 436 139 3416 5.5 1 3019 397 140 2425 5.5 1 2035 390 141 1720 5.5 1 1298 422 142 1467 5.5 1 1047 420 143 1384 5.5 1 919 465 144 1554 5.5 1 998 556 145 1687 5.5 1 968 719 146 2051 5.5 1 1114 937 147 2872 5.5 1 1385 1487 148 5820 5.5 1 2576 3244 149 14836 5.5 1 6249 8587 150 49326 5.5 1 21035 28291 151 19045 5.5 1 6985 12060 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001.fastq.gz ============================================= 372443998 sequences processed in total