SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_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-8to10kb-4_S16_L004_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.76 s (33 us/read; 1.81 M reads/minute). === Summary === Total reads processed: 263,614 Reads with adapters: 63,442 (24.1%) Reads written (passing filters): 263,614 (100.0%) Total basepairs processed: 32,676,756 bp Quality-trimmed: 3,323,211 bp (10.2%) Total written (filtered): 29,151,359 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 63442 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 25.6% G: 13.9% T: 28.5% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 46329 65903.5 0 46329 2 10984 16475.9 0 10984 3 2673 4119.0 0 2673 4 938 1029.7 0 938 5 212 257.4 0 212 6 51 64.4 0 51 7 59 16.1 0 59 8 20 4.0 0 20 9 8 1.0 0 7 1 10 38 0.3 1 17 21 11 7 0.1 1 2 5 12 32 0.0 1 14 18 13 16 0.0 1 5 11 14 49 0.0 1 32 17 15 14 0.0 1 11 3 16 7 0.0 1 3 4 17 37 0.0 1 27 10 18 5 0.0 1 3 2 19 24 0.0 1 14 10 20 20 0.0 1 14 6 21 3 0.0 1 1 2 22 1 0.0 1 0 1 23 19 0.0 1 11 8 24 65 0.0 1 43 22 25 20 0.0 1 14 6 26 25 0.0 1 14 11 27 5 0.0 1 3 2 28 24 0.0 1 12 12 29 3 0.0 1 2 1 30 22 0.0 1 14 8 31 2 0.0 1 2 32 32 0.0 1 22 10 33 37 0.0 1 28 9 34 3 0.0 1 1 2 35 15 0.0 1 10 5 36 12 0.0 1 6 6 37 21 0.0 1 14 7 38 14 0.0 1 11 3 39 19 0.0 1 14 5 40 8 0.0 1 4 4 41 29 0.0 1 21 8 42 48 0.0 1 31 17 43 10 0.0 1 7 3 44 23 0.0 1 17 6 45 53 0.0 1 37 16 46 23 0.0 1 13 10 47 4 0.0 1 3 1 48 46 0.0 1 42 4 49 24 0.0 1 17 7 50 17 0.0 1 13 4 51 105 0.0 1 86 19 52 23 0.0 1 17 6 53 15 0.0 1 13 2 54 15 0.0 1 13 2 55 20 0.0 1 15 5 56 13 0.0 1 11 2 57 28 0.0 1 20 8 58 33 0.0 1 23 10 59 21 0.0 1 17 4 60 28 0.0 1 19 9 61 24 0.0 1 20 4 62 27 0.0 1 21 6 63 29 0.0 1 25 4 64 34 0.0 1 24 10 65 48 0.0 1 33 15 66 45 0.0 1 35 10 67 70 0.0 1 58 12 68 160 0.0 1 142 18 69 98 0.0 1 84 14 70 48 0.0 1 38 10 71 21 0.0 1 19 2 72 17 0.0 1 12 5 73 13 0.0 1 10 3 74 7 0.0 1 7 75 7 0.0 1 6 1 76 9 0.0 1 7 2 77 9 0.0 1 4 5 78 21 0.0 1 11 10 79 11 0.0 1 7 4 80 10 0.0 1 5 5 81 8 0.0 1 3 5 82 8 0.0 1 6 2 83 13 0.0 1 12 1 84 7 0.0 1 4 3 85 10 0.0 1 10 86 4 0.0 1 2 2 87 10 0.0 1 8 2 88 5 0.0 1 5 89 6 0.0 1 5 1 90 8 0.0 1 6 2 91 4 0.0 1 3 1 92 6 0.0 1 6 93 7 0.0 1 5 2 94 9 0.0 1 7 2 95 5 0.0 1 4 1 96 5 0.0 1 4 1 97 7 0.0 1 6 1 98 11 0.0 1 7 4 99 8 0.0 1 7 1 100 3 0.0 1 3 101 4 0.0 1 3 1 102 10 0.0 1 7 3 103 11 0.0 1 6 5 104 2 0.0 1 1 1 105 6 0.0 1 4 2 106 3 0.0 1 1 2 107 4 0.0 1 3 1 108 5 0.0 1 3 2 109 8 0.0 1 6 2 110 3 0.0 1 2 1 111 4 0.0 1 4 112 7 0.0 1 5 2 113 8 0.0 1 7 1 114 5 0.0 1 4 1 115 7 0.0 1 5 2 116 3 0.0 1 2 1 117 6 0.0 1 1 5 118 6 0.0 1 3 3 119 4 0.0 1 3 1 120 3 0.0 1 1 2 121 5 0.0 1 2 3 122 4 0.0 1 3 1 123 1 0.0 1 0 1 124 5 0.0 1 5 125 2 0.0 1 2 126 5 0.0 1 4 1 127 2 0.0 1 0 2 128 1 0.0 1 1 129 1 0.0 1 1 131 1 0.0 1 1 136 1 0.0 1 0 1 140 1 0.0 1 1 150 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001.fastq.gz ============================================= 263614 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 263614 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 54408 (20.64%)