SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_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-5to7kb-3_S11_L003_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 31.06 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 991,000 Reads with adapters: 208,477 (21.0%) Reads written (passing filters): 991,000 (100.0%) Total basepairs processed: 116,898,739 bp Quality-trimmed: 22,202,813 bp (19.0%) Total written (filtered): 94,271,187 bp (80.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 208477 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.5% C: 28.3% G: 14.0% T: 27.8% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 152478 247750.0 0 152478 2 40714 61937.5 0 40714 3 8464 15484.4 0 8464 4 3191 3871.1 0 3191 5 653 967.8 0 653 6 108 241.9 0 108 7 66 60.5 0 66 8 41 15.1 0 41 9 18 3.8 0 10 8 10 44 0.9 1 20 24 11 13 0.2 1 3 10 12 32 0.1 1 17 15 13 19 0.0 1 9 10 14 72 0.0 1 38 34 15 22 0.0 1 10 12 16 12 0.0 1 6 6 17 40 0.0 1 22 18 18 11 0.0 1 5 6 19 31 0.0 1 19 12 20 19 0.0 1 13 6 21 1 0.0 1 1 22 6 0.0 1 5 1 23 20 0.0 1 12 8 24 78 0.0 1 43 35 25 40 0.0 1 16 24 26 31 0.0 1 19 12 27 2 0.0 1 1 1 28 30 0.0 1 20 10 29 5 0.0 1 2 3 30 32 0.0 1 19 13 31 5 0.0 1 2 3 32 42 0.0 1 28 14 33 48 0.0 1 33 15 34 7 0.0 1 2 5 35 20 0.0 1 5 15 36 19 0.0 1 15 4 37 36 0.0 1 27 9 38 10 0.0 1 7 3 39 18 0.0 1 9 9 40 11 0.0 1 5 6 41 33 0.0 1 18 15 42 69 0.0 1 47 22 43 15 0.0 1 8 7 44 25 0.0 1 14 11 45 58 0.0 1 37 21 46 18 0.0 1 10 8 47 14 0.0 1 8 6 48 57 0.0 1 37 20 49 42 0.0 1 26 16 50 24 0.0 1 15 9 51 152 0.0 1 107 45 52 38 0.0 1 21 17 53 23 0.0 1 18 5 54 14 0.0 1 12 2 55 46 0.0 1 34 12 56 16 0.0 1 12 4 57 37 0.0 1 25 12 58 38 0.0 1 28 10 59 22 0.0 1 15 7 60 41 0.0 1 27 14 61 34 0.0 1 20 14 62 33 0.0 1 19 14 63 39 0.0 1 26 13 64 52 0.0 1 43 9 65 51 0.0 1 42 9 66 49 0.0 1 38 11 67 88 0.0 1 65 23 68 274 0.0 1 237 37 69 121 0.0 1 108 13 70 50 0.0 1 42 8 71 27 0.0 1 22 5 72 9 0.0 1 5 4 73 16 0.0 1 7 9 74 17 0.0 1 13 4 75 9 0.0 1 6 3 76 7 0.0 1 2 5 77 7 0.0 1 6 1 78 9 0.0 1 7 2 79 14 0.0 1 7 7 80 9 0.0 1 7 2 81 8 0.0 1 4 4 82 5 0.0 1 3 2 83 11 0.0 1 7 4 84 7 0.0 1 7 85 7 0.0 1 4 3 86 10 0.0 1 6 4 87 12 0.0 1 6 6 88 4 0.0 1 2 2 89 5 0.0 1 3 2 90 7 0.0 1 3 4 91 5 0.0 1 2 3 92 4 0.0 1 3 1 93 3 0.0 1 1 2 94 6 0.0 1 5 1 95 4 0.0 1 3 1 96 7 0.0 1 5 2 97 9 0.0 1 5 4 98 9 0.0 1 6 3 99 3 0.0 1 2 1 100 8 0.0 1 1 7 101 10 0.0 1 2 8 102 5 0.0 1 3 2 103 4 0.0 1 2 2 104 6 0.0 1 3 3 105 5 0.0 1 4 1 106 3 0.0 1 1 2 107 4 0.0 1 0 4 108 5 0.0 1 3 2 109 3 0.0 1 2 1 110 5 0.0 1 3 2 111 4 0.0 1 1 3 112 3 0.0 1 2 1 113 8 0.0 1 4 4 114 4 0.0 1 2 2 115 3 0.0 1 3 116 6 0.0 1 0 6 117 5 0.0 1 3 2 118 3 0.0 1 1 2 119 2 0.0 1 1 1 120 6 0.0 1 4 2 121 2 0.0 1 2 122 6 0.0 1 2 4 123 4 0.0 1 2 2 124 3 0.0 1 1 2 125 1 0.0 1 0 1 126 2 0.0 1 1 1 127 5 0.0 1 1 4 128 2 0.0 1 1 1 129 1 0.0 1 1 130 3 0.0 1 2 1 131 1 0.0 1 0 1 132 1 0.0 1 0 1 133 1 0.0 1 1 134 2 0.0 1 0 2 138 1 0.0 1 1 142 1 0.0 1 0 1 145 1 0.0 1 0 1 146 1 0.0 1 0 1 150 2 0.0 1 0 2 151 3 0.0 1 1 2 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001.fastq.gz ============================================= 991000 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 991000 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 222638 (22.47%)