SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-8_S30_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-2to4kb-8_S30_L008_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 15.37 s (30 us/read; 1.99 M reads/minute). === Summary === Total reads processed: 510,999 Reads with adapters: 111,846 (21.9%) Reads written (passing filters): 510,999 (100.0%) Total basepairs processed: 60,454,446 bp Quality-trimmed: 2,368,086 bp (3.9%) Total written (filtered): 57,827,278 bp (95.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 111846 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 23.5% G: 14.1% T: 29.3% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 82925 127749.8 0 82925 2 19968 31937.4 0 19968 3 4929 7984.4 0 4929 4 2047 1996.1 0 2047 5 420 499.0 0 420 6 57 124.8 0 57 7 28 31.2 0 28 8 17 7.8 0 17 9 2 1.9 0 1 1 10 17 0.5 1 5 12 11 5 0.1 1 3 2 12 6 0.0 1 4 2 13 3 0.0 1 2 1 14 8 0.0 1 6 2 15 7 0.0 1 6 1 16 4 0.0 1 3 1 17 4 0.0 1 0 4 18 12 0.0 1 8 4 19 9 0.0 1 7 2 20 7 0.0 1 2 5 21 1 0.0 1 1 22 12 0.0 1 9 3 23 5 0.0 1 2 3 24 10 0.0 1 10 25 4 0.0 1 3 1 26 4 0.0 1 3 1 27 8 0.0 1 6 2 28 13 0.0 1 10 3 29 1 0.0 1 1 30 6 0.0 1 3 3 31 12 0.0 1 7 5 32 7 0.0 1 5 2 33 6 0.0 1 5 1 34 14 0.0 1 10 4 35 5 0.0 1 5 36 9 0.0 1 0 9 37 6 0.0 1 4 2 38 15 0.0 1 13 2 39 4 0.0 1 3 1 40 2 0.0 1 0 2 41 8 0.0 1 7 1 42 6 0.0 1 4 2 43 4 0.0 1 4 44 3 0.0 1 3 45 3 0.0 1 2 1 46 5 0.0 1 3 2 47 9 0.0 1 8 1 48 7 0.0 1 4 3 49 4 0.0 1 1 3 50 2 0.0 1 2 51 10 0.0 1 7 3 52 11 0.0 1 9 2 53 6 0.0 1 1 5 54 8 0.0 1 6 2 55 20 0.0 1 16 4 56 8 0.0 1 6 2 57 7 0.0 1 2 5 58 8 0.0 1 4 4 59 2 0.0 1 1 1 60 5 0.0 1 3 2 61 13 0.0 1 12 1 62 7 0.0 1 5 2 63 3 0.0 1 3 64 6 0.0 1 6 65 14 0.0 1 10 4 66 11 0.0 1 8 3 67 4 0.0 1 3 1 68 9 0.0 1 8 1 69 9 0.0 1 7 2 70 7 0.0 1 6 1 71 13 0.0 1 10 3 72 20 0.0 1 10 10 73 31 0.0 1 14 17 74 107 0.0 1 35 72 75 226 0.0 1 149 77 76 99 0.0 1 74 25 77 72 0.0 1 48 24 78 45 0.0 1 31 14 79 33 0.0 1 22 11 80 16 0.0 1 5 11 81 18 0.0 1 12 6 82 11 0.0 1 8 3 83 6 0.0 1 4 2 84 7 0.0 1 3 4 85 6 0.0 1 3 3 86 2 0.0 1 1 1 87 4 0.0 1 2 2 88 1 0.0 1 0 1 89 6 0.0 1 3 3 90 7 0.0 1 4 3 91 6 0.0 1 3 3 92 9 0.0 1 5 4 93 4 0.0 1 3 1 94 5 0.0 1 3 2 95 6 0.0 1 4 2 96 5 0.0 1 4 1 97 1 0.0 1 0 1 98 1 0.0 1 0 1 99 5 0.0 1 5 100 3 0.0 1 2 1 101 2 0.0 1 2 102 4 0.0 1 3 1 103 6 0.0 1 3 3 104 1 0.0 1 1 105 5 0.0 1 4 1 106 1 0.0 1 1 107 3 0.0 1 2 1 108 5 0.0 1 3 2 110 1 0.0 1 1 111 3 0.0 1 2 1 112 4 0.0 1 3 1 114 2 0.0 1 2 115 2 0.0 1 1 1 117 3 0.0 1 3 118 1 0.0 1 1 121 3 0.0 1 1 2 123 2 0.0 1 2 124 2 0.0 1 2 125 1 0.0 1 1 126 1 0.0 1 1 127 1 0.0 1 1 128 2 0.0 1 2 130 1 0.0 1 1 131 1 0.0 1 1 132 2 0.0 1 2 135 2 0.0 1 2 136 2 0.0 1 2 137 3 0.0 1 1 2 138 6 0.0 1 6 139 1 0.0 1 0 1 140 1 0.0 1 1 141 1 0.0 1 1 142 1 0.0 1 1 144 3 0.0 1 2 1 145 3 0.0 1 1 2 146 4 0.0 1 4 147 4 0.0 1 4 148 12 0.0 1 5 7 149 21 0.0 1 11 10 150 78 0.0 1 31 47 151 32 0.0 1 12 20 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001.fastq.gz ============================================= 510999 sequences processed in total