SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_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_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.47 s (32 us/read; 1.89 M reads/minute). === Summary === Total reads processed: 266,864 Reads with adapters: 56,715 (21.3%) Reads written (passing filters): 266,864 (100.0%) Total basepairs processed: 31,541,791 bp Quality-trimmed: 5,198,294 bp (16.5%) Total written (filtered): 26,213,777 bp (83.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 56715 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 25.6% G: 13.3% T: 30.4% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 42033 66716.0 0 42033 2 10351 16679.0 0 10351 3 2329 4169.8 0 2329 4 905 1042.4 0 905 5 171 260.6 0 171 6 25 65.2 0 25 7 13 16.3 0 13 8 4 4.1 0 4 9 6 1.0 0 4 2 10 16 0.3 1 5 11 11 6 0.1 1 3 3 12 8 0.0 1 5 3 13 1 0.0 1 1 14 13 0.0 1 6 7 15 4 0.0 1 3 1 16 5 0.0 1 3 2 17 5 0.0 1 4 1 18 3 0.0 1 2 1 19 7 0.0 1 4 3 20 6 0.0 1 3 3 21 1 0.0 1 1 22 2 0.0 1 2 23 2 0.0 1 2 24 15 0.0 1 6 9 25 5 0.0 1 2 3 26 5 0.0 1 4 1 27 1 0.0 1 1 28 10 0.0 1 5 5 29 2 0.0 1 0 2 30 7 0.0 1 5 2 32 3 0.0 1 1 2 33 11 0.0 1 9 2 34 1 0.0 1 0 1 35 5 0.0 1 4 1 36 3 0.0 1 2 1 37 4 0.0 1 4 38 1 0.0 1 1 39 3 0.0 1 2 1 40 3 0.0 1 0 3 41 8 0.0 1 6 2 42 10 0.0 1 6 4 43 1 0.0 1 0 1 44 6 0.0 1 6 45 9 0.0 1 7 2 46 9 0.0 1 7 2 47 3 0.0 1 1 2 48 14 0.0 1 11 3 49 4 0.0 1 3 1 50 3 0.0 1 3 51 13 0.0 1 9 4 52 7 0.0 1 3 4 53 1 0.0 1 1 54 6 0.0 1 4 2 55 7 0.0 1 4 3 56 1 0.0 1 1 57 6 0.0 1 3 3 58 12 0.0 1 4 8 59 8 0.0 1 5 3 60 5 0.0 1 4 1 61 6 0.0 1 4 2 62 11 0.0 1 9 2 63 10 0.0 1 10 64 11 0.0 1 9 2 65 7 0.0 1 5 2 66 10 0.0 1 8 2 67 129 0.0 1 5 124 68 181 0.0 1 72 109 69 49 0.0 1 27 22 70 35 0.0 1 4 31 71 14 0.0 1 8 6 72 3 0.0 1 2 1 73 6 0.0 1 4 2 74 3 0.0 1 1 2 75 5 0.0 1 1 4 76 1 0.0 1 1 77 2 0.0 1 0 2 78 1 0.0 1 1 79 1 0.0 1 1 81 3 0.0 1 3 82 2 0.0 1 2 83 2 0.0 1 2 84 2 0.0 1 0 2 85 2 0.0 1 0 2 86 2 0.0 1 0 2 87 1 0.0 1 1 88 3 0.0 1 2 1 89 1 0.0 1 0 1 90 4 0.0 1 3 1 91 4 0.0 1 2 2 94 2 0.0 1 1 1 95 1 0.0 1 1 96 3 0.0 1 1 2 97 2 0.0 1 0 2 98 2 0.0 1 0 2 99 1 0.0 1 0 1 100 2 0.0 1 0 2 101 1 0.0 1 0 1 102 1 0.0 1 0 1 103 1 0.0 1 0 1 105 2 0.0 1 0 2 106 1 0.0 1 0 1 107 1 0.0 1 1 109 1 0.0 1 1 110 1 0.0 1 1 111 2 0.0 1 1 1 116 1 0.0 1 0 1 117 1 0.0 1 1 118 2 0.0 1 2 119 1 0.0 1 0 1 122 1 0.0 1 1 123 1 0.0 1 0 1 125 1 0.0 1 0 1 126 1 0.0 1 1 127 1 0.0 1 0 1 128 1 0.0 1 0 1 129 3 0.0 1 2 1 132 1 0.0 1 1 133 1 0.0 1 0 1 140 1 0.0 1 0 1 143 1 0.0 1 0 1 147 1 0.0 1 0 1 148 3 0.0 1 1 2 149 2 0.0 1 1 1 150 20 0.0 1 3 17 151 8 0.0 1 2 6 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001.fastq.gz ============================================= 266864 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 266864 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 62879 (23.56%)