SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2_S5_L002_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-2_S5_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 12501.20 s (33 us/read; 1.81 M reads/minute). === Summary === Total reads processed: 377,072,437 Reads with adapters: 90,631,124 (24.0%) Reads written (passing filters): 377,072,437 (100.0%) Total basepairs processed: 47,112,865,190 bp Quality-trimmed: 4,195,593,705 bp (8.9%) Total written (filtered): 42,680,315,285 bp (90.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 90631124 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: 0.2% Overview of removed sequences length count expect max.err error counts 1 67152818 94268109.2 0 67152818 2 15748176 23567027.3 0 15748176 3 3788674 5891756.8 0 3788674 4 1384657 1472939.2 0 1384657 5 287354 368234.8 0 287354 6 54417 92058.7 0 54417 7 53824 23014.7 0 53824 8 25265 5753.7 0 25265 9 7882 1438.4 0 4984 2898 10 31538 359.6 1 14504 17034 11 10978 89.9 1 4147 6831 12 22103 22.5 1 12260 9843 13 11948 5.6 1 5748 6200 14 53231 5.6 1 33382 19849 15 12018 5.6 1 7003 5015 16 9117 5.6 1 4686 4431 17 32326 5.6 1 20206 12120 18 4822 5.6 1 2305 2517 19 23821 5.6 1 15385 8436 20 14814 5.6 1 9370 5444 21 2436 5.6 1 940 1496 22 4481 5.6 1 1954 2527 23 19477 5.6 1 11809 7668 24 61787 5.6 1 39034 22753 25 20247 5.6 1 12882 7365 26 21997 5.6 1 15138 6859 27 3295 5.6 1 1601 1694 28 22239 5.6 1 14341 7898 29 4554 5.6 1 2205 2349 30 27879 5.6 1 18279 9600 31 5564 5.6 1 2977 2587 32 30724 5.6 1 20708 10016 33 36426 5.6 1 26925 9501 34 3917 5.6 1 1925 1992 35 14871 5.6 1 8320 6551 36 14804 5.6 1 8924 5880 37 20116 5.6 1 14415 5701 38 12855 5.6 1 7768 5087 39 12166 5.6 1 8356 3810 40 5775 5.6 1 3236 2539 41 21594 5.6 1 14613 6981 42 52025 5.6 1 36005 16020 43 6670 5.6 1 3964 2706 44 24528 5.6 1 16837 7691 45 58551 5.6 1 41318 17233 46 15568 5.6 1 10495 5073 47 5432 5.6 1 3204 2228 48 43088 5.6 1 31161 11927 49 27430 5.6 1 19432 7998 50 12194 5.6 1 7796 4398 51 118875 5.6 1 88524 30351 52 22499 5.6 1 15146 7353 53 13243 5.6 1 8952 4291 54 12204 5.6 1 8664 3540 55 26276 5.6 1 19001 7275 56 17531 5.6 1 12483 5048 57 18297 5.6 1 13543 4754 58 26014 5.6 1 19831 6183 59 18164 5.6 1 13440 4724 60 17905 5.6 1 13569 4336 61 22547 5.6 1 17175 5372 62 24706 5.6 1 18974 5732 63 25196 5.6 1 19514 5682 64 25230 5.6 1 19457 5773 65 30391 5.6 1 23718 6673 66 40115 5.6 1 31365 8750 67 103771 5.6 1 54118 49653 68 220604 5.6 1 169116 51488 69 98530 5.6 1 80632 17898 70 33662 5.6 1 24339 9323 71 18916 5.6 1 12965 5951 72 12525 5.6 1 8293 4232 73 11480 5.6 1 7594 3886 74 9599 5.6 1 6411 3188 75 8603 5.6 1 5549 3054 76 8199 5.6 1 5256 2943 77 8271 5.6 1 5381 2890 78 8408 5.6 1 5289 3119 79 8640 5.6 1 5466 3174 80 8641 5.6 1 5474 3167 81 8351 5.6 1 5268 3083 82 7973 5.6 1 5108 2865 83 7765 5.6 1 4854 2911 84 7419 5.6 1 4648 2771 85 7071 5.6 1 4399 2672 86 7120 5.6 1 4319 2801 87 6865 5.6 1 4175 2690 88 6837 5.6 1 4233 2604 89 6834 5.6 1 4175 2659 90 6332 5.6 1 3908 2424 91 6085 5.6 1 3779 2306 92 6171 5.6 1 3771 2400 93 5759 5.6 1 3448 2311 94 5959 5.6 1 3670 2289 95 5979 5.6 1 3628 2351 96 5736 5.6 1 3542 2194 97 5757 5.6 1 3483 2274 98 6317 5.6 1 3931 2386 99 6126 5.6 1 3776 2350 100 6122 5.6 1 3849 2273 101 6038 5.6 1 3783 2255 102 5989 5.6 1 3765 2224 103 5786 5.6 1 3634 2152 104 5753 5.6 1 3655 2098 105 5674 5.6 1 3567 2107 106 5536 5.6 1 3495 2041 107 5168 5.6 1 3266 1902 108 5107 5.6 1 3273 1834 109 4885 5.6 1 3082 1803 110 4943 5.6 1 3119 1824 111 4731 5.6 1 2958 1773 112 4603 5.6 1 2934 1669 113 4346 5.6 1 2732 1614 114 4311 5.6 1 2743 1568 115 4202 5.6 1 2677 1525 116 4098 5.6 1 2516 1582 117 3717 5.6 1 2351 1366 118 3626 5.6 1 2263 1363 119 3472 5.6 1 2147 1325 120 3235 5.6 1 2021 1214 121 3090 5.6 1 1956 1134 122 2917 5.6 1 1802 1115 123 2749 5.6 1 1672 1077 124 2550 5.6 1 1539 1011 125 2330 5.6 1 1426 904 126 2036 5.6 1 1224 812 127 1707 5.6 1 994 713 128 1477 5.6 1 846 631 129 1283 5.6 1 690 593 130 1021 5.6 1 569 452 131 872 5.6 1 451 421 132 686 5.6 1 346 340 133 584 5.6 1 282 302 134 488 5.6 1 225 263 135 414 5.6 1 181 233 136 313 5.6 1 137 176 137 261 5.6 1 102 159 138 206 5.6 1 81 125 139 188 5.6 1 70 118 140 167 5.6 1 50 117 141 156 5.6 1 41 115 142 150 5.6 1 36 114 143 122 5.6 1 36 86 144 153 5.6 1 44 109 145 159 5.6 1 42 117 146 188 5.6 1 47 141 147 261 5.6 1 71 190 148 801 5.6 1 243 558 149 2340 5.6 1 630 1710 150 9887 5.6 1 2687 7200 151 2255 5.6 1 638 1617 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2_S5_L002_R2_001.fastq.gz ============================================= 377072437 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 377072437 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 78553966 (20.83%)