SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_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-7_S27_L007_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 10.26 s (33 us/read; 1.82 M reads/minute). === Summary === Total reads processed: 311,953 Reads with adapters: 67,501 (21.6%) Reads written (passing filters): 311,953 (100.0%) Total basepairs processed: 36,501,373 bp Quality-trimmed: 6,452,319 bp (17.7%) Total written (filtered): 29,887,216 bp (81.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 67501 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.3% C: 26.4% G: 13.7% T: 28.3% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 1 49440 77988.2 0 49440 2 12901 19497.1 0 12901 3 2780 4874.3 0 2780 4 1060 1218.6 0 1060 5 201 304.6 0 201 6 26 76.2 0 26 7 15 19.0 0 15 8 10 4.8 0 10 9 4 1.2 0 0 4 10 9 0.3 1 3 6 11 3 0.1 1 2 1 12 6 0.0 1 0 6 13 5 0.0 1 4 1 14 12 0.0 1 10 2 15 3 0.0 1 2 1 16 5 0.0 1 2 3 17 4 0.0 1 3 1 18 3 0.0 1 3 19 4 0.0 1 3 1 20 6 0.0 1 3 3 23 2 0.0 1 2 24 11 0.0 1 5 6 25 5 0.0 1 4 1 26 11 0.0 1 9 2 28 4 0.0 1 2 2 30 4 0.0 1 3 1 31 1 0.0 1 1 32 5 0.0 1 3 2 33 9 0.0 1 7 2 34 1 0.0 1 0 1 35 2 0.0 1 1 1 36 1 0.0 1 0 1 37 2 0.0 1 1 1 38 1 0.0 1 1 39 1 0.0 1 1 40 1 0.0 1 1 41 3 0.0 1 2 1 42 8 0.0 1 5 3 44 7 0.0 1 6 1 45 12 0.0 1 9 3 46 1 0.0 1 0 1 47 1 0.0 1 1 48 6 0.0 1 4 2 49 1 0.0 1 0 1 50 3 0.0 1 3 51 13 0.0 1 9 4 52 10 0.0 1 7 3 53 2 0.0 1 2 54 3 0.0 1 2 1 55 6 0.0 1 3 3 56 6 0.0 1 4 2 57 7 0.0 1 5 2 58 5 0.0 1 3 2 59 7 0.0 1 6 1 60 2 0.0 1 2 61 2 0.0 1 2 62 5 0.0 1 4 1 63 3 0.0 1 2 1 64 7 0.0 1 5 2 65 8 0.0 1 4 4 66 9 0.0 1 7 2 67 256 0.0 1 11 245 68 255 0.0 1 66 189 69 73 0.0 1 28 45 70 41 0.0 1 6 35 71 17 0.0 1 3 14 72 16 0.0 1 1 15 73 6 0.0 1 2 4 74 6 0.0 1 2 4 76 1 0.0 1 0 1 77 3 0.0 1 1 2 78 1 0.0 1 1 79 3 0.0 1 1 2 80 2 0.0 1 0 2 81 1 0.0 1 0 1 82 2 0.0 1 1 1 83 1 0.0 1 1 85 2 0.0 1 2 87 2 0.0 1 0 2 88 2 0.0 1 1 1 89 2 0.0 1 0 2 90 2 0.0 1 0 2 91 5 0.0 1 1 4 92 1 0.0 1 1 93 1 0.0 1 1 95 2 0.0 1 0 2 96 2 0.0 1 0 2 97 1 0.0 1 1 98 1 0.0 1 0 1 99 3 0.0 1 1 2 101 4 0.0 1 3 1 103 1 0.0 1 1 104 1 0.0 1 0 1 105 3 0.0 1 1 2 107 2 0.0 1 2 108 1 0.0 1 0 1 111 1 0.0 1 0 1 112 2 0.0 1 1 1 116 1 0.0 1 1 122 1 0.0 1 0 1 123 1 0.0 1 1 124 1 0.0 1 0 1 127 2 0.0 1 2 130 2 0.0 1 2 131 1 0.0 1 1 133 1 0.0 1 0 1 135 1 0.0 1 1 137 1 0.0 1 0 1 139 1 0.0 1 0 1 142 1 0.0 1 1 144 1 0.0 1 1 147 2 0.0 1 0 2 149 7 0.0 1 1 6 150 47 0.0 1 9 38 151 10 0.0 1 1 9 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001.fastq.gz ============================================= 311953 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 311953 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 73249 (23.48%)