SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_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-8_S30_L008_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 15.95 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 510,999 Reads with adapters: 116,745 (22.8%) Reads written (passing filters): 510,999 (100.0%) Total basepairs processed: 60,905,950 bp Quality-trimmed: 6,222,214 bp (10.2%) Total written (filtered): 54,387,931 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 116745 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 25.7% G: 13.8% T: 28.9% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 85527 127749.8 0 85527 2 21610 31937.4 0 21610 3 4908 7984.4 0 4908 4 1850 1996.1 0 1850 5 366 499.0 0 366 6 68 124.8 0 68 7 62 31.2 0 62 8 33 7.8 0 33 9 3 1.9 0 1 2 10 34 0.5 1 15 19 11 13 0.1 1 4 9 12 19 0.0 1 10 9 13 7 0.0 1 2 5 14 48 0.0 1 26 22 15 13 0.0 1 10 3 16 5 0.0 1 2 3 17 24 0.0 1 14 10 18 2 0.0 1 0 2 19 15 0.0 1 6 9 20 14 0.0 1 10 4 22 7 0.0 1 1 6 23 15 0.0 1 10 5 24 47 0.0 1 35 12 25 18 0.0 1 12 6 26 12 0.0 1 10 2 27 5 0.0 1 2 3 28 11 0.0 1 9 2 29 1 0.0 1 0 1 30 16 0.0 1 14 2 31 3 0.0 1 1 2 32 29 0.0 1 21 8 33 37 0.0 1 31 6 34 1 0.0 1 0 1 35 7 0.0 1 3 4 36 6 0.0 1 3 3 37 17 0.0 1 10 7 38 7 0.0 1 5 2 39 15 0.0 1 12 3 40 3 0.0 1 2 1 41 15 0.0 1 13 2 42 36 0.0 1 21 15 43 3 0.0 1 1 2 44 20 0.0 1 11 9 45 38 0.0 1 27 11 46 15 0.0 1 13 2 47 6 0.0 1 4 2 48 34 0.0 1 27 7 49 20 0.0 1 16 4 50 11 0.0 1 6 5 51 72 0.0 1 52 20 52 16 0.0 1 12 4 53 10 0.0 1 8 2 54 17 0.0 1 13 4 55 23 0.0 1 16 7 56 15 0.0 1 10 5 57 16 0.0 1 15 1 58 20 0.0 1 15 5 59 19 0.0 1 19 60 18 0.0 1 15 3 61 23 0.0 1 16 7 62 29 0.0 1 24 5 63 18 0.0 1 12 6 64 16 0.0 1 12 4 65 23 0.0 1 18 5 66 31 0.0 1 25 6 67 196 0.0 1 36 160 68 426 0.0 1 338 88 69 177 0.0 1 112 65 70 96 0.0 1 70 26 71 41 0.0 1 32 9 72 19 0.0 1 9 10 73 19 0.0 1 14 5 74 9 0.0 1 4 5 75 7 0.0 1 3 4 76 6 0.0 1 5 1 77 7 0.0 1 4 3 78 12 0.0 1 7 5 79 4 0.0 1 1 3 80 8 0.0 1 7 1 81 7 0.0 1 3 4 82 10 0.0 1 5 5 83 6 0.0 1 3 3 84 4 0.0 1 3 1 85 11 0.0 1 6 5 86 6 0.0 1 4 2 87 3 0.0 1 3 88 5 0.0 1 3 2 89 4 0.0 1 0 4 90 5 0.0 1 1 4 91 11 0.0 1 4 7 92 7 0.0 1 6 1 93 3 0.0 1 0 3 94 8 0.0 1 6 2 95 9 0.0 1 4 5 96 6 0.0 1 4 2 97 6 0.0 1 4 2 98 8 0.0 1 4 4 99 3 0.0 1 2 1 100 6 0.0 1 3 3 101 3 0.0 1 1 2 102 6 0.0 1 3 3 103 2 0.0 1 2 104 5 0.0 1 3 2 105 4 0.0 1 1 3 106 3 0.0 1 2 1 107 4 0.0 1 4 108 3 0.0 1 3 109 2 0.0 1 1 1 110 2 0.0 1 0 2 111 4 0.0 1 2 2 112 5 0.0 1 3 2 113 5 0.0 1 5 114 1 0.0 1 1 115 1 0.0 1 1 116 2 0.0 1 1 1 117 3 0.0 1 1 2 118 3 0.0 1 2 1 119 5 0.0 1 2 3 120 1 0.0 1 1 121 2 0.0 1 2 122 4 0.0 1 3 1 123 4 0.0 1 3 1 125 3 0.0 1 3 126 2 0.0 1 1 1 128 1 0.0 1 1 129 1 0.0 1 1 130 1 0.0 1 0 1 131 2 0.0 1 2 132 1 0.0 1 0 1 133 2 0.0 1 1 1 134 1 0.0 1 1 135 1 0.0 1 1 140 1 0.0 1 1 141 1 0.0 1 0 1 143 1 0.0 1 1 145 1 0.0 1 1 147 1 0.0 1 0 1 148 3 0.0 1 2 1 149 7 0.0 1 4 3 150 32 0.0 1 10 22 151 12 0.0 1 4 8 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001.fastq.gz ============================================= 510999 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 510999 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 123040 (24.08%)