SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_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-8_S31_L008_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 12.98 s (38 us/read; 1.58 M reads/minute). === Summary === Total reads processed: 341,141 Reads with adapters: 79,138 (23.2%) Reads written (passing filters): 341,141 (100.0%) Total basepairs processed: 44,015,343 bp Quality-trimmed: 1,267,590 bp (2.9%) Total written (filtered): 42,567,682 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 79138 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.3% C: 23.7% G: 13.5% T: 28.5% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 61157 85285.2 0 61157 2 12269 21321.3 0 12269 3 3268 5330.3 0 3268 4 1226 1332.6 0 1226 5 241 333.1 0 241 6 40 83.3 0 40 7 6 20.8 0 6 8 3 5.2 0 3 9 3 1.3 0 0 3 10 11 0.3 1 3 8 11 1 0.1 1 1 12 2 0.0 1 1 1 13 5 0.0 1 2 3 14 1 0.0 1 1 15 4 0.0 1 2 2 16 1 0.0 1 0 1 18 3 0.0 1 2 1 19 2 0.0 1 2 20 2 0.0 1 0 2 22 5 0.0 1 4 1 23 2 0.0 1 0 2 24 2 0.0 1 2 25 1 0.0 1 1 26 2 0.0 1 1 1 27 1 0.0 1 0 1 28 4 0.0 1 3 1 30 1 0.0 1 1 31 3 0.0 1 2 1 32 1 0.0 1 0 1 33 2 0.0 1 2 34 1 0.0 1 1 35 1 0.0 1 1 36 2 0.0 1 2 37 5 0.0 1 4 1 38 2 0.0 1 1 1 39 5 0.0 1 4 1 40 1 0.0 1 0 1 41 6 0.0 1 6 42 2 0.0 1 1 1 43 3 0.0 1 2 1 44 1 0.0 1 1 46 2 0.0 1 2 47 1 0.0 1 1 49 2 0.0 1 1 1 51 2 0.0 1 2 52 1 0.0 1 0 1 53 4 0.0 1 3 1 55 6 0.0 1 6 56 4 0.0 1 4 57 3 0.0 1 1 2 58 1 0.0 1 1 59 6 0.0 1 6 61 1 0.0 1 1 63 3 0.0 1 3 64 2 0.0 1 2 66 6 0.0 1 4 2 67 3 0.0 1 2 1 68 1 0.0 1 1 69 5 0.0 1 3 2 70 1 0.0 1 1 71 3 0.0 1 3 72 2 0.0 1 1 1 73 9 0.0 1 4 5 74 9 0.0 1 3 6 75 178 0.0 1 10 168 76 149 0.0 1 30 119 77 77 0.0 1 19 58 78 63 0.0 1 17 46 79 22 0.0 1 6 16 80 18 0.0 1 5 13 81 13 0.0 1 6 7 82 6 0.0 1 0 6 83 7 0.0 1 0 7 84 4 0.0 1 2 2 85 6 0.0 1 3 3 86 6 0.0 1 1 5 87 3 0.0 1 2 1 88 6 0.0 1 0 6 89 3 0.0 1 2 1 90 5 0.0 1 1 4 91 1 0.0 1 1 92 4 0.0 1 1 3 93 4 0.0 1 0 4 94 3 0.0 1 0 3 95 1 0.0 1 1 96 1 0.0 1 0 1 97 1 0.0 1 0 1 98 1 0.0 1 0 1 99 2 0.0 1 0 2 100 2 0.0 1 0 2 101 1 0.0 1 1 102 1 0.0 1 0 1 103 1 0.0 1 0 1 104 1 0.0 1 0 1 105 1 0.0 1 0 1 106 1 0.0 1 0 1 107 3 0.0 1 0 3 109 2 0.0 1 0 2 110 4 0.0 1 0 4 111 1 0.0 1 0 1 114 1 0.0 1 1 119 1 0.0 1 1 122 1 0.0 1 1 126 1 0.0 1 1 127 2 0.0 1 1 1 130 2 0.0 1 1 1 132 1 0.0 1 0 1 133 1 0.0 1 0 1 134 1 0.0 1 1 135 1 0.0 1 0 1 136 2 0.0 1 1 1 140 1 0.0 1 0 1 141 2 0.0 1 0 2 142 2 0.0 1 0 2 143 1 0.0 1 0 1 144 2 0.0 1 1 1 145 1 0.0 1 0 1 146 4 0.0 1 1 3 147 2 0.0 1 0 2 148 11 0.0 1 1 10 149 27 0.0 1 2 25 150 64 0.0 1 6 58 151 30 0.0 1 5 25 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001.fastq.gz ============================================= 341141 sequences processed in total