SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_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-5to7kb-3_S11_L003_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 40.71 s (41 us/read; 1.46 M reads/minute). === Summary === Total reads processed: 991,000 Reads with adapters: 224,438 (22.6%) Reads written (passing filters): 991,000 (100.0%) Total basepairs processed: 132,025,856 bp Quality-trimmed: 3,692,130 bp (2.8%) Total written (filtered): 128,002,352 bp (97.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 224438 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 25.4% G: 13.7% T: 28.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 174859 247750.0 0 174859 2 35877 61937.5 0 35877 3 9006 15484.4 0 9006 4 3130 3871.1 0 3130 5 617 967.8 0 617 6 132 241.9 0 132 7 33 60.5 0 33 8 13 15.1 0 13 9 8 3.8 0 3 5 10 26 0.9 1 3 23 11 7 0.2 1 2 5 12 13 0.1 1 8 5 13 15 0.0 1 10 5 14 7 0.0 1 4 3 15 8 0.0 1 5 3 16 4 0.0 1 1 3 17 4 0.0 1 1 3 18 20 0.0 1 9 11 19 13 0.0 1 5 8 20 3 0.0 1 2 1 21 4 0.0 1 2 2 22 9 0.0 1 4 5 23 10 0.0 1 4 6 24 8 0.0 1 5 3 25 8 0.0 1 4 4 26 3 0.0 1 1 2 27 10 0.0 1 8 2 28 20 0.0 1 6 14 29 9 0.0 1 3 6 30 11 0.0 1 3 8 31 8 0.0 1 2 6 32 10 0.0 1 6 4 33 4 0.0 1 2 2 34 17 0.0 1 10 7 35 6 0.0 1 4 2 36 6 0.0 1 1 5 37 4 0.0 1 1 3 38 13 0.0 1 9 4 39 12 0.0 1 10 2 40 10 0.0 1 4 6 41 14 0.0 1 8 6 42 13 0.0 1 8 5 43 4 0.0 1 3 1 44 2 0.0 1 2 45 5 0.0 1 0 5 46 5 0.0 1 2 3 47 2 0.0 1 2 48 10 0.0 1 8 2 49 9 0.0 1 7 2 50 2 0.0 1 1 1 51 3 0.0 1 2 1 52 5 0.0 1 4 1 53 7 0.0 1 3 4 54 6 0.0 1 4 2 55 19 0.0 1 13 6 56 6 0.0 1 1 5 57 9 0.0 1 5 4 58 5 0.0 1 5 59 6 0.0 1 4 2 60 8 0.0 1 6 2 61 1 0.0 1 1 62 9 0.0 1 3 6 63 7 0.0 1 6 1 64 3 0.0 1 1 2 65 9 0.0 1 7 2 66 16 0.0 1 8 8 67 12 0.0 1 8 4 68 5 0.0 1 4 1 69 11 0.0 1 9 2 70 7 0.0 1 5 2 71 8 0.0 1 7 1 72 10 0.0 1 6 4 73 13 0.0 1 10 3 74 12 0.0 1 8 4 75 31 0.0 1 12 19 76 37 0.0 1 29 8 77 16 0.0 1 9 7 78 9 0.0 1 4 5 79 9 0.0 1 3 6 80 7 0.0 1 5 2 81 3 0.0 1 1 2 82 2 0.0 1 1 1 83 2 0.0 1 2 85 3 0.0 1 2 1 86 3 0.0 1 0 3 87 2 0.0 1 1 1 88 2 0.0 1 0 2 90 5 0.0 1 1 4 91 2 0.0 1 0 2 92 1 0.0 1 1 93 1 0.0 1 0 1 94 2 0.0 1 2 95 2 0.0 1 0 2 96 1 0.0 1 0 1 97 2 0.0 1 2 99 2 0.0 1 0 2 100 1 0.0 1 1 101 4 0.0 1 0 4 102 3 0.0 1 2 1 105 1 0.0 1 1 106 1 0.0 1 1 107 1 0.0 1 0 1 109 1 0.0 1 1 111 1 0.0 1 0 1 112 2 0.0 1 0 2 113 2 0.0 1 0 2 114 2 0.0 1 2 115 1 0.0 1 1 116 2 0.0 1 0 2 117 1 0.0 1 0 1 119 1 0.0 1 0 1 121 2 0.0 1 0 2 123 4 0.0 1 2 2 124 1 0.0 1 1 125 2 0.0 1 2 126 2 0.0 1 1 1 130 2 0.0 1 1 1 131 2 0.0 1 2 134 1 0.0 1 1 137 1 0.0 1 0 1 139 1 0.0 1 0 1 141 1 0.0 1 0 1 142 1 0.0 1 1 143 1 0.0 1 0 1 145 1 0.0 1 1 148 2 0.0 1 1 1 149 1 0.0 1 0 1 150 3 0.0 1 2 1 151 2 0.0 1 1 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001.fastq.gz ============================================= 991000 sequences processed in total