SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_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-5to7kb-5_S19_L005_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9609.88 s (29 us/read; 2.09 M reads/minute). === Summary === Total reads processed: 334,676,537 Reads with adapters: 75,529,864 (22.6%) Reads written (passing filters): 334,676,537 (100.0%) Total basepairs processed: 37,650,893,595 bp Quality-trimmed: 3,667,776,006 bp (9.7%) Total written (filtered): 33,645,292,032 bp (89.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 75529864 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.3% C: 25.1% G: 14.2% T: 28.9% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 52899788 83669134.2 0 52899788 2 14026357 20917283.6 0 14026357 3 3149311 5229320.9 0 3149311 4 1299949 1307330.2 0 1299949 5 274100 326832.6 0 274100 6 47719 81708.1 0 47719 7 51314 20427.0 0 51314 8 32241 5106.8 0 32241 9 7160 1276.7 0 4983 2177 10 29839 319.2 1 15654 14185 11 9518 79.8 1 3980 5538 12 21007 19.9 1 13129 7878 13 12246 5.0 1 6364 5882 14 49771 5.0 1 34512 15259 15 14776 5.0 1 10000 4776 16 10524 5.0 1 6082 4442 17 31867 5.0 1 22443 9424 18 5650 5.0 1 3093 2557 19 27602 5.0 1 20046 7556 20 22139 5.0 1 16372 5767 21 2688 5.0 1 1094 1594 22 4562 5.0 1 2116 2446 23 22033 5.0 1 15019 7014 24 54775 5.0 1 38293 16482 25 21035 5.0 1 14912 6123 26 30011 5.0 1 23700 6311 27 3259 5.0 1 1609 1650 28 22829 5.0 1 16216 6613 29 4058 5.0 1 2053 2005 30 23914 5.0 1 16939 6975 31 6039 5.0 1 3654 2385 32 30384 5.0 1 22413 7971 33 56837 5.0 1 46299 10538 34 3908 5.0 1 2020 1888 35 10892 5.0 1 6038 4854 36 10338 5.0 1 6259 4079 37 28511 5.0 1 22626 5885 38 11097 5.0 1 6857 4240 39 16072 5.0 1 12306 3766 40 7287 5.0 1 4229 3058 41 26370 5.0 1 19241 7129 42 44150 5.0 1 33043 11107 43 8048 5.0 1 5498 2550 44 27440 5.0 1 20243 7197 45 43337 5.0 1 32849 10488 46 20454 5.0 1 15751 4703 47 7316 5.0 1 4599 2717 48 49782 5.0 1 38054 11728 49 27998 5.0 1 21117 6881 50 15085 5.0 1 9846 5239 51 93014 5.0 1 71821 21193 52 20416 5.0 1 14651 5765 53 14291 5.0 1 10322 3969 54 20910 5.0 1 16929 3981 55 31429 5.0 1 23949 7480 56 16314 5.0 1 11622 4692 57 26790 5.0 1 21077 5713 58 37293 5.0 1 30323 6970 59 23880 5.0 1 18851 5029 60 23305 5.0 1 18743 4562 61 23531 5.0 1 18932 4599 62 25868 5.0 1 20687 5181 63 31520 5.0 1 25411 6109 64 35337 5.0 1 28547 6790 65 38804 5.0 1 31084 7720 66 44830 5.0 1 34313 10517 67 340055 5.0 1 50118 289937 68 756436 5.0 1 486254 270182 69 399520 5.0 1 310962 88558 70 151584 5.0 1 85909 65675 71 88846 5.0 1 59718 29128 72 39750 5.0 1 24713 15037 73 24746 5.0 1 15748 8998 74 16698 5.0 1 10465 6233 75 14585 5.0 1 8916 5669 76 13690 5.0 1 8615 5075 77 12248 5.0 1 7410 4838 78 12124 5.0 1 7386 4738 79 11799 5.0 1 7261 4538 80 11412 5.0 1 6931 4481 81 11400 5.0 1 7045 4355 82 11240 5.0 1 7080 4160 83 10426 5.0 1 6498 3928 84 9978 5.0 1 6294 3684 85 9812 5.0 1 6166 3646 86 9378 5.0 1 5998 3380 87 9004 5.0 1 5646 3358 88 9461 5.0 1 5828 3633 89 9434 5.0 1 5758 3676 90 9378 5.0 1 5877 3501 91 9007 5.0 1 5500 3507 92 8650 5.0 1 5451 3199 93 8259 5.0 1 5097 3162 94 8348 5.0 1 5260 3088 95 7563 5.0 1 4609 2954 96 7765 5.0 1 4812 2953 97 7584 5.0 1 4769 2815 98 6956 5.0 1 4348 2608 99 7376 5.0 1 4598 2778 100 7722 5.0 1 5001 2721 101 7521 5.0 1 4884 2637 102 7357 5.0 1 4778 2579 103 7420 5.0 1 4856 2564 104 7401 5.0 1 4928 2473 105 7162 5.0 1 4835 2327 106 7074 5.0 1 4747 2327 107 7153 5.0 1 4939 2214 108 6957 5.0 1 4752 2205 109 6708 5.0 1 4681 2027 110 6480 5.0 1 4485 1995 111 6317 5.0 1 4396 1921 112 6048 5.0 1 4239 1809 113 5740 5.0 1 3931 1809 114 5521 5.0 1 3837 1684 115 5148 5.0 1 3501 1647 116 5161 5.0 1 3589 1572 117 4981 5.0 1 3433 1548 118 4965 5.0 1 3431 1534 119 4590 5.0 1 3127 1463 120 4481 5.0 1 3079 1402 121 4150 5.0 1 2890 1260 122 4103 5.0 1 2805 1298 123 3851 5.0 1 2630 1221 124 3739 5.0 1 2569 1170 125 3457 5.0 1 2426 1031 126 3343 5.0 1 2378 965 127 3067 5.0 1 2182 885 128 3541 5.0 1 2699 842 129 2605 5.0 1 1875 730 130 2604 5.0 1 1939 665 131 1923 5.0 1 1419 504 132 1899 5.0 1 1366 533 133 1661 5.0 1 1184 477 134 1604 5.0 1 1147 457 135 1419 5.0 1 1005 414 136 1368 5.0 1 946 422 137 1230 5.0 1 837 393 138 1165 5.0 1 801 364 139 1120 5.0 1 726 394 140 1093 5.0 1 678 415 141 1012 5.0 1 565 447 142 1120 5.0 1 606 514 143 1017 5.0 1 499 518 144 1057 5.0 1 489 568 145 1063 5.0 1 412 651 146 1210 5.0 1 424 786 147 1728 5.0 1 509 1219 148 5293 5.0 1 1487 3806 149 15622 5.0 1 4285 11337 150 66322 5.0 1 17669 48653 151 18140 5.0 1 4703 13437 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001.fastq.gz ============================================= 334676537 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 334676537 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 98853907 (29.54%)