SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_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-4_S16_L004_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.71 s (33 us/read; 1.82 M reads/minute). === Summary === Total reads processed: 263,614 Reads with adapters: 59,745 (22.7%) Reads written (passing filters): 263,614 (100.0%) Total basepairs processed: 32,701,025 bp Quality-trimmed: 1,097,320 bp (3.4%) Total written (filtered): 31,486,211 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 59745 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.2% C: 23.7% G: 13.7% T: 29.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 45424 65903.5 0 45424 2 9848 16475.9 0 9848 3 2585 4119.0 0 2585 4 983 1029.7 0 983 5 192 257.4 0 192 6 24 64.4 0 24 7 23 16.1 0 23 8 5 4.0 0 5 9 2 1.0 0 1 1 10 12 0.3 1 6 6 11 1 0.1 1 1 12 6 0.0 1 4 2 13 6 0.0 1 3 3 14 6 0.0 1 4 2 15 7 0.0 1 5 2 16 8 0.0 1 6 2 18 11 0.0 1 7 4 19 11 0.0 1 10 1 20 3 0.0 1 2 1 21 2 0.0 1 1 1 22 4 0.0 1 4 23 5 0.0 1 3 2 24 9 0.0 1 5 4 25 4 0.0 1 0 4 26 9 0.0 1 7 2 27 6 0.0 1 4 2 28 6 0.0 1 5 1 29 5 0.0 1 3 2 30 4 0.0 1 1 3 31 1 0.0 1 1 32 6 0.0 1 2 4 33 6 0.0 1 3 3 34 12 0.0 1 11 1 35 6 0.0 1 4 2 36 7 0.0 1 4 3 37 9 0.0 1 7 2 38 6 0.0 1 4 2 39 8 0.0 1 5 3 40 7 0.0 1 3 4 41 6 0.0 1 5 1 42 7 0.0 1 4 3 43 5 0.0 1 4 1 44 7 0.0 1 6 1 45 10 0.0 1 8 2 46 1 0.0 1 1 47 4 0.0 1 2 2 48 6 0.0 1 2 4 49 5 0.0 1 4 1 50 6 0.0 1 5 1 51 4 0.0 1 3 1 52 6 0.0 1 5 1 53 8 0.0 1 8 54 16 0.0 1 12 4 55 4 0.0 1 3 1 56 12 0.0 1 10 2 57 8 0.0 1 8 58 8 0.0 1 6 2 59 7 0.0 1 5 2 60 12 0.0 1 11 1 61 3 0.0 1 1 2 62 4 0.0 1 4 63 9 0.0 1 5 4 64 6 0.0 1 5 1 65 8 0.0 1 5 3 66 6 0.0 1 6 67 17 0.0 1 14 3 68 3 0.0 1 3 69 5 0.0 1 5 70 10 0.0 1 7 3 71 6 0.0 1 3 3 72 5 0.0 1 4 1 73 10 0.0 1 6 4 74 6 0.0 1 6 75 11 0.0 1 7 4 76 9 0.0 1 8 1 77 35 0.0 1 34 1 78 20 0.0 1 12 8 79 17 0.0 1 11 6 80 10 0.0 1 9 1 81 7 0.0 1 6 1 82 4 0.0 1 2 2 83 2 0.0 1 1 1 84 5 0.0 1 2 3 85 3 0.0 1 3 86 5 0.0 1 4 1 87 6 0.0 1 0 6 88 2 0.0 1 1 1 89 2 0.0 1 1 1 90 1 0.0 1 1 91 2 0.0 1 2 92 3 0.0 1 2 1 93 6 0.0 1 4 2 94 1 0.0 1 0 1 95 4 0.0 1 3 1 96 6 0.0 1 4 2 97 4 0.0 1 3 1 99 3 0.0 1 3 100 5 0.0 1 4 1 101 3 0.0 1 3 102 1 0.0 1 0 1 103 2 0.0 1 1 1 104 1 0.0 1 0 1 105 3 0.0 1 2 1 107 2 0.0 1 0 2 108 1 0.0 1 1 110 5 0.0 1 3 2 111 1 0.0 1 0 1 112 2 0.0 1 1 1 113 5 0.0 1 4 1 115 3 0.0 1 2 1 116 1 0.0 1 1 117 1 0.0 1 0 1 118 3 0.0 1 3 119 2 0.0 1 1 1 120 1 0.0 1 0 1 121 1 0.0 1 0 1 122 1 0.0 1 1 123 2 0.0 1 1 1 126 1 0.0 1 0 1 127 3 0.0 1 2 1 128 1 0.0 1 0 1 130 1 0.0 1 1 131 1 0.0 1 1 138 1 0.0 1 0 1 142 1 0.0 1 1 143 1 0.0 1 0 1 149 1 0.0 1 1 151 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001.fastq.gz ============================================= 263614 sequences processed in total