SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_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-5_S18_L005_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9.84 s (37 us/read; 1.63 M reads/minute). === Summary === Total reads processed: 266,864 Reads with adapters: 66,657 (25.0%) Reads written (passing filters): 266,864 (100.0%) Total basepairs processed: 33,661,250 bp Quality-trimmed: 1,161,529 bp (3.5%) Total written (filtered): 32,363,429 bp (96.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 66657 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.2% C: 22.7% G: 13.5% T: 28.1% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 51635 66716.0 0 51635 2 10308 16679.0 0 10308 3 2918 4169.8 0 2918 4 992 1042.4 0 992 5 157 260.6 0 157 6 25 65.2 0 25 7 6 16.3 0 6 8 4 4.1 0 4 9 1 1.0 0 0 1 10 8 0.3 1 6 2 11 2 0.1 1 0 2 12 1 0.0 1 1 13 1 0.0 1 0 1 14 3 0.0 1 1 2 15 3 0.0 1 3 17 1 0.0 1 0 1 18 3 0.0 1 1 2 19 3 0.0 1 2 1 22 4 0.0 1 1 3 23 3 0.0 1 1 2 24 5 0.0 1 4 1 25 2 0.0 1 1 1 26 3 0.0 1 1 2 27 2 0.0 1 2 28 2 0.0 1 2 30 4 0.0 1 2 2 31 3 0.0 1 2 1 32 2 0.0 1 2 33 2 0.0 1 2 34 5 0.0 1 3 2 35 3 0.0 1 3 36 6 0.0 1 1 5 37 3 0.0 1 3 38 1 0.0 1 1 39 2 0.0 1 2 41 10 0.0 1 6 4 42 4 0.0 1 4 43 4 0.0 1 4 44 3 0.0 1 2 1 45 1 0.0 1 1 47 1 0.0 1 0 1 48 2 0.0 1 2 49 1 0.0 1 1 50 1 0.0 1 1 51 3 0.0 1 3 52 4 0.0 1 1 3 54 1 0.0 1 1 55 7 0.0 1 7 56 2 0.0 1 2 57 1 0.0 1 0 1 59 2 0.0 1 0 2 61 2 0.0 1 1 1 62 3 0.0 1 3 63 1 0.0 1 0 1 64 2 0.0 1 0 2 65 1 0.0 1 1 66 3 0.0 1 3 67 2 0.0 1 1 1 68 2 0.0 1 1 1 69 4 0.0 1 4 70 4 0.0 1 3 1 71 4 0.0 1 4 72 2 0.0 1 1 1 73 6 0.0 1 5 1 74 10 0.0 1 5 5 75 73 0.0 1 7 66 76 82 0.0 1 20 62 77 43 0.0 1 13 30 78 38 0.0 1 14 24 79 20 0.0 1 5 15 80 11 0.0 1 4 7 81 5 0.0 1 1 4 82 4 0.0 1 2 2 83 2 0.0 1 0 2 84 3 0.0 1 1 2 85 1 0.0 1 0 1 86 2 0.0 1 1 1 87 2 0.0 1 1 1 88 2 0.0 1 1 1 89 1 0.0 1 0 1 90 2 0.0 1 1 1 91 1 0.0 1 1 92 2 0.0 1 1 1 93 2 0.0 1 0 2 95 4 0.0 1 0 4 96 1 0.0 1 1 98 3 0.0 1 2 1 99 3 0.0 1 1 2 100 2 0.0 1 2 103 2 0.0 1 1 1 104 2 0.0 1 2 105 2 0.0 1 2 111 2 0.0 1 1 1 112 1 0.0 1 1 113 1 0.0 1 0 1 115 2 0.0 1 2 117 1 0.0 1 1 118 1 0.0 1 0 1 119 1 0.0 1 1 121 1 0.0 1 1 122 3 0.0 1 2 1 124 1 0.0 1 0 1 126 2 0.0 1 1 1 128 2 0.0 1 1 1 129 1 0.0 1 1 130 4 0.0 1 2 2 131 1 0.0 1 1 134 1 0.0 1 1 135 2 0.0 1 2 138 1 0.0 1 0 1 139 1 0.0 1 0 1 140 1 0.0 1 0 1 141 1 0.0 1 1 142 1 0.0 1 1 143 1 0.0 1 1 145 1 0.0 1 0 1 146 1 0.0 1 1 147 3 0.0 1 2 1 148 5 0.0 1 0 5 149 11 0.0 1 2 9 150 48 0.0 1 7 41 151 24 0.0 1 5 19 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001.fastq.gz ============================================= 266864 sequences processed in total