SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-7_S26_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-2to4kb-7_S26_L007_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 15.01 s (30 us/read; 1.99 M reads/minute). === Summary === Total reads processed: 498,123 Reads with adapters: 109,256 (21.9%) Reads written (passing filters): 498,123 (100.0%) Total basepairs processed: 58,840,808 bp Quality-trimmed: 2,336,141 bp (4.0%) Total written (filtered): 56,251,464 bp (95.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 109256 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.4% C: 23.3% G: 14.3% T: 29.5% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 80908 124530.8 0 80908 2 19555 31132.7 0 19555 3 4911 7783.2 0 4911 4 1960 1945.8 0 1960 5 402 486.4 0 402 6 45 121.6 0 45 7 19 30.4 0 19 8 19 7.6 0 19 9 3 1.9 0 0 3 10 14 0.5 1 1 13 12 14 0.0 1 10 4 13 6 0.0 1 4 2 14 9 0.0 1 5 4 15 7 0.0 1 5 2 16 5 0.0 1 4 1 17 2 0.0 1 1 1 18 17 0.0 1 13 4 19 21 0.0 1 21 20 3 0.0 1 2 1 21 4 0.0 1 1 3 22 8 0.0 1 5 3 23 4 0.0 1 3 1 24 9 0.0 1 7 2 25 3 0.0 1 2 1 26 6 0.0 1 1 5 27 10 0.0 1 8 2 28 8 0.0 1 7 1 29 1 0.0 1 1 30 4 0.0 1 2 2 31 10 0.0 1 8 2 32 5 0.0 1 3 2 33 5 0.0 1 5 34 5 0.0 1 3 2 35 3 0.0 1 1 2 36 9 0.0 1 7 2 37 3 0.0 1 3 38 12 0.0 1 10 2 39 5 0.0 1 3 2 40 10 0.0 1 8 2 41 8 0.0 1 8 42 10 0.0 1 8 2 43 1 0.0 1 0 1 44 1 0.0 1 1 45 3 0.0 1 2 1 46 2 0.0 1 2 47 10 0.0 1 9 1 48 5 0.0 1 4 1 49 3 0.0 1 2 1 50 7 0.0 1 6 1 51 12 0.0 1 8 4 52 7 0.0 1 4 3 53 13 0.0 1 5 8 54 8 0.0 1 6 2 55 15 0.0 1 14 1 56 3 0.0 1 3 57 7 0.0 1 6 1 58 6 0.0 1 6 59 3 0.0 1 3 60 5 0.0 1 5 61 4 0.0 1 4 62 4 0.0 1 2 2 63 5 0.0 1 4 1 64 7 0.0 1 5 2 65 21 0.0 1 19 2 66 7 0.0 1 7 67 6 0.0 1 5 1 68 12 0.0 1 10 2 69 9 0.0 1 6 3 70 7 0.0 1 7 71 15 0.0 1 11 4 72 31 0.0 1 21 10 73 34 0.0 1 16 18 74 106 0.0 1 32 74 75 174 0.0 1 100 74 76 118 0.0 1 81 37 77 85 0.0 1 54 31 78 61 0.0 1 37 24 79 35 0.0 1 16 19 80 14 0.0 1 11 3 81 9 0.0 1 4 5 82 7 0.0 1 4 3 83 8 0.0 1 5 3 84 5 0.0 1 3 2 85 7 0.0 1 4 3 86 9 0.0 1 4 5 87 6 0.0 1 4 2 88 6 0.0 1 2 4 89 3 0.0 1 1 2 90 5 0.0 1 4 1 91 7 0.0 1 4 3 92 6 0.0 1 4 2 93 3 0.0 1 2 1 94 2 0.0 1 2 95 5 0.0 1 2 3 96 4 0.0 1 2 2 97 3 0.0 1 1 2 98 6 0.0 1 4 2 99 7 0.0 1 6 1 100 3 0.0 1 1 2 101 3 0.0 1 3 102 4 0.0 1 2 2 103 5 0.0 1 4 1 104 5 0.0 1 4 1 105 2 0.0 1 2 106 3 0.0 1 3 107 1 0.0 1 1 108 3 0.0 1 3 109 4 0.0 1 3 1 110 4 0.0 1 3 1 111 2 0.0 1 2 112 6 0.0 1 4 2 114 1 0.0 1 1 115 2 0.0 1 0 2 116 2 0.0 1 1 1 118 2 0.0 1 2 119 2 0.0 1 1 1 122 1 0.0 1 1 124 3 0.0 1 2 1 128 1 0.0 1 1 131 4 0.0 1 3 1 132 2 0.0 1 1 1 134 1 0.0 1 1 135 2 0.0 1 1 1 136 1 0.0 1 0 1 137 4 0.0 1 4 138 1 0.0 1 1 139 4 0.0 1 4 141 1 0.0 1 0 1 142 1 0.0 1 1 143 2 0.0 1 1 1 144 1 0.0 1 0 1 145 1 0.0 1 0 1 146 1 0.0 1 0 1 147 2 0.0 1 0 2 148 8 0.0 1 4 4 149 23 0.0 1 14 9 150 75 0.0 1 24 51 151 27 0.0 1 8 19 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001.fastq.gz ============================================= 498123 sequences processed in total