SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-4_S15_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-5to7kb-4_S15_L004_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 33.99 s (41 us/read; 1.47 M reads/minute). === Summary === Total reads processed: 833,817 Reads with adapters: 187,573 (22.5%) Reads written (passing filters): 833,817 (100.0%) Total basepairs processed: 110,663,660 bp Quality-trimmed: 3,368,816 bp (3.0%) Total written (filtered): 107,020,491 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 187573 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.5% C: 25.6% G: 13.6% T: 28.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 146090 208454.2 0 146090 2 30165 52113.6 0 30165 3 7425 13028.4 0 7425 4 2678 3257.1 0 2678 5 528 814.3 0 528 6 85 203.6 0 85 7 35 50.9 0 35 8 13 12.7 0 13 9 8 3.2 0 2 6 10 20 0.8 1 0 20 11 2 0.2 1 1 1 12 3 0.0 1 1 2 13 7 0.0 1 4 3 14 5 0.0 1 1 4 15 6 0.0 1 2 4 16 1 0.0 1 1 17 2 0.0 1 1 1 18 17 0.0 1 8 9 19 10 0.0 1 4 6 20 6 0.0 1 1 5 21 2 0.0 1 0 2 22 4 0.0 1 2 2 23 1 0.0 1 1 24 4 0.0 1 2 2 25 2 0.0 1 2 26 1 0.0 1 1 27 2 0.0 1 0 2 28 9 0.0 1 4 5 29 1 0.0 1 0 1 30 5 0.0 1 4 1 31 4 0.0 1 1 3 32 6 0.0 1 5 1 33 5 0.0 1 4 1 34 5 0.0 1 3 2 35 3 0.0 1 1 2 36 9 0.0 1 4 5 37 6 0.0 1 4 2 38 5 0.0 1 4 1 39 11 0.0 1 5 6 40 3 0.0 1 1 2 41 11 0.0 1 7 4 42 4 0.0 1 4 43 13 0.0 1 9 4 44 4 0.0 1 2 2 45 2 0.0 1 0 2 46 3 0.0 1 2 1 47 3 0.0 1 1 2 48 8 0.0 1 5 3 49 8 0.0 1 7 1 50 3 0.0 1 1 2 51 4 0.0 1 2 2 52 3 0.0 1 0 3 53 4 0.0 1 3 1 54 4 0.0 1 2 2 55 15 0.0 1 11 4 56 4 0.0 1 2 2 57 6 0.0 1 2 4 58 2 0.0 1 2 59 11 0.0 1 9 2 60 9 0.0 1 3 6 61 2 0.0 1 2 62 9 0.0 1 7 2 63 13 0.0 1 6 7 64 7 0.0 1 7 65 5 0.0 1 5 66 12 0.0 1 9 3 67 10 0.0 1 4 6 68 5 0.0 1 5 69 4 0.0 1 3 1 70 2 0.0 1 2 71 6 0.0 1 5 1 72 5 0.0 1 3 2 73 13 0.0 1 9 4 74 10 0.0 1 9 1 75 16 0.0 1 6 10 76 18 0.0 1 10 8 77 18 0.0 1 13 5 78 14 0.0 1 10 4 79 11 0.0 1 6 5 80 4 0.0 1 3 1 81 4 0.0 1 3 1 82 2 0.0 1 0 2 83 1 0.0 1 1 84 1 0.0 1 1 85 1 0.0 1 1 86 3 0.0 1 3 87 1 0.0 1 0 1 88 2 0.0 1 2 89 4 0.0 1 4 91 2 0.0 1 1 1 92 1 0.0 1 1 93 1 0.0 1 0 1 94 2 0.0 1 1 1 95 1 0.0 1 0 1 96 2 0.0 1 1 1 98 1 0.0 1 0 1 99 2 0.0 1 0 2 102 3 0.0 1 1 2 103 2 0.0 1 2 104 2 0.0 1 2 105 1 0.0 1 0 1 106 2 0.0 1 1 1 109 4 0.0 1 2 2 110 2 0.0 1 0 2 111 1 0.0 1 1 112 2 0.0 1 0 2 114 1 0.0 1 0 1 116 1 0.0 1 0 1 118 1 0.0 1 0 1 120 2 0.0 1 1 1 121 1 0.0 1 0 1 123 1 0.0 1 0 1 124 1 0.0 1 0 1 127 1 0.0 1 1 128 2 0.0 1 0 2 129 1 0.0 1 1 132 1 0.0 1 1 137 1 0.0 1 0 1 144 1 0.0 1 0 1 148 1 0.0 1 0 1 150 4 0.0 1 1 3 151 4 0.0 1 3 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001.fastq.gz ============================================= 833817 sequences processed in total