SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_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-8to10kb-6_S24_L006_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 4.21 s (42 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 99,111 Reads with adapters: 23,804 (24.0%) Reads written (passing filters): 99,111 (100.0%) Total basepairs processed: 12,944,228 bp Quality-trimmed: 339,740 bp (2.6%) Total written (filtered): 12,558,590 bp (97.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23804 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.9% C: 22.6% G: 13.1% T: 28.9% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 18504 24777.8 0 18504 2 3686 6194.4 0 3686 3 1014 1548.6 0 1014 4 336 387.2 0 336 5 60 96.8 0 60 6 6 24.2 0 6 7 5 6.0 0 5 8 3 1.5 0 3 9 1 0.4 0 1 10 4 0.1 1 0 4 13 1 0.0 1 1 16 1 0.0 1 1 18 2 0.0 1 2 22 1 0.0 1 1 25 2 0.0 1 0 2 26 1 0.0 1 0 1 27 2 0.0 1 1 1 29 1 0.0 1 1 34 3 0.0 1 1 2 37 1 0.0 1 1 38 1 0.0 1 1 41 4 0.0 1 2 2 44 1 0.0 1 0 1 48 1 0.0 1 0 1 53 1 0.0 1 1 55 1 0.0 1 1 57 2 0.0 1 2 58 1 0.0 1 1 62 1 0.0 1 1 64 1 0.0 1 1 65 1 0.0 1 1 66 2 0.0 1 2 69 1 0.0 1 0 1 70 1 0.0 1 1 72 1 0.0 1 0 1 73 1 0.0 1 1 74 2 0.0 1 1 1 75 15 0.0 1 1 14 76 33 0.0 1 7 26 77 21 0.0 1 7 14 78 16 0.0 1 5 11 79 10 0.0 1 4 6 80 6 0.0 1 3 3 81 2 0.0 1 0 2 82 1 0.0 1 0 1 83 2 0.0 1 1 1 84 2 0.0 1 0 2 86 1 0.0 1 1 88 2 0.0 1 0 2 91 1 0.0 1 1 95 1 0.0 1 0 1 97 2 0.0 1 0 2 100 1 0.0 1 0 1 101 1 0.0 1 1 108 1 0.0 1 0 1 113 1 0.0 1 0 1 120 1 0.0 1 0 1 126 1 0.0 1 1 129 1 0.0 1 1 132 1 0.0 1 0 1 135 1 0.0 1 1 140 2 0.0 1 1 1 144 1 0.0 1 1 147 1 0.0 1 1 149 2 0.0 1 0 2 150 10 0.0 1 4 6 151 7 0.0 1 2 5 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001.fastq.gz ============================================= 99111 sequences processed in total