SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-7_S25_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-7_S25_L007_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.69 s (55 us/read; 1.09 M reads/minute). === Summary === Total reads processed: 12,504 Reads with adapters: 2,989 (23.9%) Reads written (passing filters): 12,504 (100.0%) Total basepairs processed: 1,640,714 bp Quality-trimmed: 89,348 bp (5.4%) Total written (filtered): 1,546,301 bp (94.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2989 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.6% C: 24.8% G: 15.1% T: 27.4% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 2234 3126.0 0 2234 2 568 781.5 0 568 3 117 195.4 0 117 4 44 48.8 0 44 5 8 12.2 0 8 6 1 3.1 0 1 9 1 0.0 0 0 1 10 1 0.0 1 0 1 22 1 0.0 1 0 1 24 1 0.0 1 1 50 1 0.0 1 0 1 63 1 0.0 1 1 65 1 0.0 1 1 73 1 0.0 1 0 1 75 3 0.0 1 2 1 76 4 0.0 1 4 128 1 0.0 1 1 149 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-7_S25_L007_R1_001.fastq.gz ============================================= 12504 sequences processed in total