SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_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-1_S3_L001_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2.00 s (32 us/read; 1.90 M reads/minute). === Summary === Total reads processed: 63,365 Reads with adapters: 12,831 (20.2%) Reads written (passing filters): 63,365 (100.0%) Total basepairs processed: 7,558,375 bp Quality-trimmed: 2,143,772 bp (28.4%) Total written (filtered): 5,393,560 bp (71.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12831 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 27.6% G: 13.4% T: 27.8% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 9589 15841.2 0 9589 2 2369 3960.3 0 2369 3 542 990.1 0 542 4 203 247.5 0 203 5 36 61.9 0 36 6 6 15.5 0 6 7 3 3.9 0 3 8 1 1.0 0 1 9 1 0.2 0 1 10 2 0.1 1 0 2 11 1 0.0 1 1 12 1 0.0 1 0 1 13 1 0.0 1 0 1 14 4 0.0 1 2 2 15 1 0.0 1 1 17 1 0.0 1 1 18 1 0.0 1 1 20 1 0.0 1 1 23 3 0.0 1 1 2 24 2 0.0 1 0 2 33 1 0.0 1 0 1 34 1 0.0 1 0 1 38 2 0.0 1 2 39 1 0.0 1 1 41 2 0.0 1 2 42 1 0.0 1 1 44 1 0.0 1 0 1 45 2 0.0 1 2 46 1 0.0 1 0 1 48 1 0.0 1 1 49 3 0.0 1 3 50 1 0.0 1 1 51 8 0.0 1 6 2 52 1 0.0 1 0 1 53 2 0.0 1 1 1 55 2 0.0 1 1 1 56 1 0.0 1 1 57 5 0.0 1 1 4 58 1 0.0 1 1 61 1 0.0 1 1 62 1 0.0 1 1 63 1 0.0 1 0 1 64 1 0.0 1 1 66 7 0.0 1 5 2 67 2 0.0 1 2 68 7 0.0 1 6 1 69 1 0.0 1 1 77 1 0.0 1 1 78 1 0.0 1 1 121 1 0.0 1 0 1 122 1 0.0 1 1 130 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001.fastq.gz ============================================= 63365 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 63365 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17074 (26.95%)