SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-1_S1_L001_R2_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_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 12233.40 s (33 us/read; 1.81 M reads/minute). === Summary === Total reads processed: 368,469,262 Reads with adapters: 88,605,467 (24.0%) Reads written (passing filters): 368,469,262 (100.0%) Total basepairs processed: 46,158,097,968 bp Quality-trimmed: 4,390,806,671 bp (9.5%) Total written (filtered): 41,536,295,439 bp (90.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 88605467 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.8% C: 25.1% G: 13.7% T: 28.1% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 65740285 92117315.5 0 65740285 2 15310568 23029328.9 0 15310568 3 3699552 5757332.2 0 3699552 4 1349516 1439333.1 0 1349516 5 280042 359833.3 0 280042 6 54063 89958.3 0 54063 7 53552 22489.6 0 53552 8 25896 5622.4 0 25896 9 7592 1405.6 0 4838 2754 10 31511 351.4 1 14585 16926 11 10878 87.8 1 4113 6765 12 21755 22.0 1 12048 9707 13 11806 5.5 1 5665 6141 14 52990 5.5 1 33226 19764 15 11900 5.5 1 6995 4905 16 9003 5.5 1 4601 4402 17 31943 5.5 1 20109 11834 18 4889 5.5 1 2384 2505 19 23859 5.5 1 15464 8395 20 14748 5.5 1 9334 5414 21 2440 5.5 1 923 1517 22 4358 5.5 1 1903 2455 23 19518 5.5 1 11813 7705 24 60756 5.5 1 38897 21859 25 20234 5.5 1 12826 7408 26 22166 5.5 1 15403 6763 27 3223 5.5 1 1544 1679 28 22240 5.5 1 14538 7702 29 4345 5.5 1 2143 2202 30 27352 5.5 1 17936 9416 31 5432 5.5 1 2955 2477 32 30622 5.5 1 20696 9926 33 37132 5.5 1 27497 9635 34 3901 5.5 1 1921 1980 35 14695 5.5 1 8281 6414 36 14479 5.5 1 8893 5586 37 20236 5.5 1 14546 5690 38 12760 5.5 1 7828 4932 39 11769 5.5 1 8146 3623 40 5516 5.5 1 3036 2480 41 21439 5.5 1 14446 6993 42 51416 5.5 1 35373 16043 43 6835 5.5 1 4021 2814 44 24467 5.5 1 16615 7852 45 56425 5.5 1 39901 16524 46 15638 5.5 1 10646 4992 47 5353 5.5 1 3093 2260 48 42292 5.5 1 30662 11630 49 26694 5.5 1 19124 7570 50 12014 5.5 1 7546 4468 51 115500 5.5 1 86303 29197 52 22315 5.5 1 15081 7234 53 13235 5.5 1 9133 4102 54 12421 5.5 1 8936 3485 55 25968 5.5 1 18923 7045 56 17229 5.5 1 12332 4897 57 18075 5.5 1 13486 4589 58 26177 5.5 1 20050 6127 59 18716 5.5 1 14087 4629 60 17611 5.5 1 13199 4412 61 22687 5.5 1 17156 5531 62 24504 5.5 1 18927 5577 63 25300 5.5 1 19549 5751 64 24998 5.5 1 19314 5684 65 29976 5.5 1 23370 6606 66 40155 5.5 1 31143 9012 67 101351 5.5 1 53700 47651 68 219942 5.5 1 170506 49436 69 92747 5.5 1 76218 16529 70 30894 5.5 1 22763 8131 71 17028 5.5 1 11820 5208 72 11714 5.5 1 7839 3875 73 10940 5.5 1 7191 3749 74 9337 5.5 1 6227 3110 75 8286 5.5 1 5433 2853 76 8030 5.5 1 5259 2771 77 7921 5.5 1 5080 2841 78 8004 5.5 1 5097 2907 79 8339 5.5 1 5380 2959 80 8238 5.5 1 5242 2996 81 7818 5.5 1 4863 2955 82 7817 5.5 1 4939 2878 83 7564 5.5 1 4811 2753 84 7173 5.5 1 4485 2688 85 6685 5.5 1 4116 2569 86 6773 5.5 1 4188 2585 87 6574 5.5 1 4065 2509 88 6452 5.5 1 4004 2448 89 6543 5.5 1 4100 2443 90 6131 5.5 1 3764 2367 91 5872 5.5 1 3624 2248 92 5998 5.5 1 3701 2297 93 5653 5.5 1 3404 2249 94 5755 5.5 1 3487 2268 95 5869 5.5 1 3640 2229 96 5451 5.5 1 3383 2068 97 5651 5.5 1 3492 2159 98 5929 5.5 1 3660 2269 99 5869 5.5 1 3637 2232 100 5789 5.5 1 3639 2150 101 5747 5.5 1 3524 2223 102 5602 5.5 1 3485 2117 103 5588 5.5 1 3540 2048 104 5387 5.5 1 3333 2054 105 5257 5.5 1 3346 1911 106 5133 5.5 1 3191 1942 107 4959 5.5 1 3156 1803 108 4732 5.5 1 3044 1688 109 4602 5.5 1 2903 1699 110 4612 5.5 1 2898 1714 111 4474 5.5 1 2807 1667 112 4252 5.5 1 2742 1510 113 4055 5.5 1 2595 1460 114 3927 5.5 1 2466 1461 115 3855 5.5 1 2462 1393 116 3792 5.5 1 2380 1412 117 3563 5.5 1 2254 1309 118 3451 5.5 1 2146 1305 119 3287 5.5 1 2035 1252 120 3092 5.5 1 1917 1175 121 3009 5.5 1 1917 1092 122 2662 5.5 1 1622 1040 123 2591 5.5 1 1604 987 124 2494 5.5 1 1532 962 125 2158 5.5 1 1332 826 126 1949 5.5 1 1112 837 127 1574 5.5 1 965 609 128 1378 5.5 1 781 597 129 1178 5.5 1 625 553 130 876 5.5 1 467 409 131 759 5.5 1 390 369 132 631 5.5 1 316 315 133 497 5.5 1 230 267 134 452 5.5 1 212 240 135 386 5.5 1 177 209 136 338 5.5 1 159 179 137 249 5.5 1 100 149 138 231 5.5 1 88 143 139 184 5.5 1 53 131 140 180 5.5 1 58 122 141 140 5.5 1 39 101 142 150 5.5 1 41 109 143 140 5.5 1 41 99 144 162 5.5 1 44 118 145 143 5.5 1 36 107 146 201 5.5 1 59 142 147 252 5.5 1 74 178 148 754 5.5 1 223 531 149 2177 5.5 1 623 1554 150 8818 5.5 1 2490 6328 151 2288 5.5 1 650 1638 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-1_S1_L001_R2_001.fastq.gz ============================================= 368469262 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 368469262 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 78087642 (21.19%)