SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-3_S12_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-8to10kb-3_S12_L003_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.75 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 258,035 Reads with adapters: 58,250 (22.6%) Reads written (passing filters): 258,035 (100.0%) Total basepairs processed: 31,975,215 bp Quality-trimmed: 1,070,389 bp (3.3%) Total written (filtered): 30,787,365 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58250 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.0% C: 23.7% G: 14.0% T: 29.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 44243 64508.8 0 44243 2 9500 16127.2 0 9500 3 2583 4031.8 0 2583 4 979 1007.9 0 979 5 224 252.0 0 224 6 31 63.0 0 31 7 17 15.7 0 17 8 6 3.9 0 6 9 1 1.0 0 1 10 11 0.2 1 7 4 11 4 0.1 1 1 3 12 3 0.0 1 1 2 13 6 0.0 1 3 3 14 4 0.0 1 1 3 15 2 0.0 1 1 1 16 2 0.0 1 0 2 17 2 0.0 1 2 18 16 0.0 1 11 5 19 8 0.0 1 4 4 20 5 0.0 1 2 3 22 10 0.0 1 7 3 23 5 0.0 1 1 4 24 7 0.0 1 6 1 25 1 0.0 1 1 27 12 0.0 1 11 1 28 10 0.0 1 6 4 29 5 0.0 1 2 3 30 5 0.0 1 3 2 31 11 0.0 1 9 2 32 9 0.0 1 7 2 33 7 0.0 1 4 3 34 8 0.0 1 4 4 35 8 0.0 1 7 1 36 4 0.0 1 3 1 37 7 0.0 1 6 1 38 6 0.0 1 4 2 39 5 0.0 1 3 2 40 8 0.0 1 6 2 41 4 0.0 1 4 42 9 0.0 1 7 2 43 8 0.0 1 4 4 44 6 0.0 1 5 1 45 6 0.0 1 6 46 5 0.0 1 3 2 47 4 0.0 1 4 48 4 0.0 1 3 1 49 11 0.0 1 7 4 50 5 0.0 1 4 1 51 1 0.0 1 1 52 4 0.0 1 4 53 8 0.0 1 6 2 54 7 0.0 1 2 5 55 4 0.0 1 3 1 56 12 0.0 1 7 5 57 6 0.0 1 6 58 6 0.0 1 5 1 59 5 0.0 1 3 2 60 11 0.0 1 6 5 61 6 0.0 1 4 2 62 4 0.0 1 3 1 63 9 0.0 1 6 3 64 3 0.0 1 3 65 6 0.0 1 5 1 66 11 0.0 1 9 2 67 11 0.0 1 9 2 68 6 0.0 1 5 1 69 2 0.0 1 1 1 70 4 0.0 1 0 4 71 6 0.0 1 5 1 72 5 0.0 1 4 1 73 9 0.0 1 7 2 74 9 0.0 1 8 1 75 13 0.0 1 12 1 76 13 0.0 1 11 2 77 38 0.0 1 31 7 78 24 0.0 1 19 5 79 13 0.0 1 11 2 80 10 0.0 1 8 2 81 5 0.0 1 3 2 82 4 0.0 1 0 4 83 5 0.0 1 4 1 84 6 0.0 1 4 2 85 2 0.0 1 2 86 6 0.0 1 2 4 87 3 0.0 1 1 2 88 5 0.0 1 5 89 1 0.0 1 1 90 4 0.0 1 2 2 91 2 0.0 1 2 92 6 0.0 1 4 2 93 6 0.0 1 3 3 95 7 0.0 1 6 1 96 3 0.0 1 1 2 97 5 0.0 1 2 3 98 4 0.0 1 3 1 99 2 0.0 1 1 1 100 2 0.0 1 2 101 4 0.0 1 0 4 102 6 0.0 1 6 103 3 0.0 1 2 1 104 4 0.0 1 2 2 105 3 0.0 1 3 106 5 0.0 1 2 3 107 1 0.0 1 1 108 4 0.0 1 3 1 109 2 0.0 1 1 1 110 1 0.0 1 1 112 2 0.0 1 0 2 113 7 0.0 1 5 2 114 2 0.0 1 2 115 1 0.0 1 1 116 2 0.0 1 2 117 3 0.0 1 2 1 119 1 0.0 1 1 121 1 0.0 1 1 122 1 0.0 1 1 123 1 0.0 1 1 124 2 0.0 1 2 128 1 0.0 1 1 129 1 0.0 1 1 134 2 0.0 1 2 135 1 0.0 1 1 136 1 0.0 1 1 137 1 0.0 1 1 145 1 0.0 1 0 1 148 2 0.0 1 0 2 150 2 0.0 1 0 2 151 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001.fastq.gz ============================================= 258035 sequences processed in total