SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-3_S9_L003_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-3_S9_L003_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2.41 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 53,313 Reads with adapters: 12,793 (24.0%) Reads written (passing filters): 53,313 (100.0%) Total basepairs processed: 7,048,549 bp Quality-trimmed: 228,714 bp (3.2%) Total written (filtered): 6,802,743 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12793 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.0% C: 24.7% G: 13.4% T: 27.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9937 13328.2 0 9937 2 2102 3332.1 0 2102 3 511 833.0 0 511 4 179 208.3 0 179 5 40 52.1 0 40 6 4 13.0 0 4 7 5 3.3 0 5 11 2 0.0 1 0 2 12 1 0.0 1 0 1 13 1 0.0 1 1 14 1 0.0 1 1 17 1 0.0 1 0 1 18 1 0.0 1 1 24 1 0.0 1 1 36 2 0.0 1 1 1 41 1 0.0 1 1 42 2 0.0 1 2 60 1 0.0 1 1 66 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-3_S9_L003_R1_001.fastq.gz ============================================= 53313 sequences processed in total