SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_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_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 12.05 s (39 us/read; 1.55 M reads/minute). === Summary === Total reads processed: 311,953 Reads with adapters: 72,500 (23.2%) Reads written (passing filters): 311,953 (100.0%) Total basepairs processed: 40,441,546 bp Quality-trimmed: 1,163,411 bp (2.9%) Total written (filtered): 39,112,230 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72500 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.2% C: 23.8% G: 13.5% T: 28.6% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 56003 77988.2 0 56003 2 11411 19497.1 0 11411 3 2963 4874.3 0 2963 4 1045 1218.6 0 1045 5 186 304.6 0 186 6 25 76.2 0 25 7 16 19.0 0 16 8 2 4.8 0 2 10 6 0.3 1 1 5 11 3 0.1 1 1 2 12 1 0.0 1 1 13 6 0.0 1 2 4 14 2 0.0 1 1 1 16 2 0.0 1 1 1 18 2 0.0 1 2 19 6 0.0 1 5 1 20 1 0.0 1 1 22 2 0.0 1 1 1 23 1 0.0 1 1 24 2 0.0 1 1 1 25 1 0.0 1 0 1 26 3 0.0 1 2 1 27 3 0.0 1 2 1 28 1 0.0 1 1 29 1 0.0 1 0 1 30 2 0.0 1 2 31 2 0.0 1 0 2 33 1 0.0 1 1 34 2 0.0 1 0 2 35 1 0.0 1 1 36 3 0.0 1 1 2 37 2 0.0 1 1 1 38 2 0.0 1 1 1 39 2 0.0 1 2 42 2 0.0 1 2 43 2 0.0 1 1 1 44 3 0.0 1 2 1 46 1 0.0 1 1 47 1 0.0 1 1 52 1 0.0 1 1 53 2 0.0 1 1 1 54 1 0.0 1 1 55 5 0.0 1 2 3 56 2 0.0 1 2 58 1 0.0 1 1 59 3 0.0 1 2 1 62 3 0.0 1 2 1 63 2 0.0 1 2 64 2 0.0 1 2 65 3 0.0 1 2 1 66 4 0.0 1 3 1 67 3 0.0 1 1 2 69 2 0.0 1 1 1 70 4 0.0 1 1 3 71 2 0.0 1 2 72 7 0.0 1 5 2 73 2 0.0 1 2 74 10 0.0 1 2 8 75 151 0.0 1 5 146 76 142 0.0 1 25 117 77 85 0.0 1 7 78 78 69 0.0 1 14 55 79 25 0.0 1 5 20 80 18 0.0 1 4 14 81 13 0.0 1 6 7 82 13 0.0 1 2 11 83 6 0.0 1 0 6 84 1 0.0 1 0 1 85 5 0.0 1 2 3 86 5 0.0 1 0 5 87 3 0.0 1 2 1 88 2 0.0 1 1 1 89 2 0.0 1 1 1 90 2 0.0 1 0 2 92 1 0.0 1 1 96 2 0.0 1 0 2 97 2 0.0 1 0 2 99 2 0.0 1 2 102 2 0.0 1 1 1 103 1 0.0 1 0 1 104 1 0.0 1 0 1 105 1 0.0 1 0 1 106 1 0.0 1 1 107 2 0.0 1 0 2 108 1 0.0 1 0 1 110 2 0.0 1 0 2 112 1 0.0 1 1 114 1 0.0 1 1 115 1 0.0 1 0 1 116 2 0.0 1 0 2 120 2 0.0 1 0 2 121 2 0.0 1 0 2 127 1 0.0 1 1 130 5 0.0 1 3 2 131 1 0.0 1 0 1 132 1 0.0 1 0 1 134 1 0.0 1 0 1 135 3 0.0 1 1 2 137 2 0.0 1 0 2 139 1 0.0 1 1 141 1 0.0 1 0 1 142 1 0.0 1 1 143 2 0.0 1 1 1 144 1 0.0 1 0 1 145 4 0.0 1 0 4 146 1 0.0 1 0 1 147 5 0.0 1 1 4 148 6 0.0 1 2 4 149 31 0.0 1 3 28 150 52 0.0 1 2 50 151 33 0.0 1 5 28 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001.fastq.gz ============================================= 311953 sequences processed in total