SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_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-8to10kb-5_S20_L005_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2.81 s (32 us/read; 1.87 M reads/minute). === Summary === Total reads processed: 87,562 Reads with adapters: 18,427 (21.0%) Reads written (passing filters): 87,562 (100.0%) Total basepairs processed: 10,025,776 bp Quality-trimmed: 1,943,431 bp (19.4%) Total written (filtered): 8,039,227 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18427 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 25.9% G: 13.5% T: 30.0% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 13325 21890.5 0 13325 2 3622 5472.6 0 3622 3 791 1368.2 0 791 4 329 342.0 0 329 5 61 85.5 0 61 6 8 21.4 0 8 7 10 5.3 0 10 8 1 1.3 0 1 9 1 0.3 0 1 10 3 0.1 1 2 1 13 2 0.0 1 0 2 14 1 0.0 1 0 1 16 2 0.0 1 1 1 17 2 0.0 1 0 2 18 1 0.0 1 0 1 20 1 0.0 1 0 1 22 1 0.0 1 0 1 23 1 0.0 1 0 1 24 2 0.0 1 2 25 2 0.0 1 2 26 1 0.0 1 1 29 2 0.0 1 1 1 30 2 0.0 1 1 1 31 3 0.0 1 2 1 32 3 0.0 1 2 1 33 4 0.0 1 3 1 35 1 0.0 1 1 37 1 0.0 1 1 38 1 0.0 1 1 41 6 0.0 1 6 44 1 0.0 1 1 45 2 0.0 1 2 46 1 0.0 1 1 47 1 0.0 1 0 1 48 2 0.0 1 2 49 3 0.0 1 3 50 2 0.0 1 1 1 51 4 0.0 1 3 1 52 3 0.0 1 2 1 53 2 0.0 1 1 1 54 4 0.0 1 4 55 1 0.0 1 0 1 56 1 0.0 1 1 57 1 0.0 1 0 1 58 4 0.0 1 2 2 59 3 0.0 1 2 1 61 1 0.0 1 0 1 62 4 0.0 1 2 2 63 2 0.0 1 2 64 2 0.0 1 1 1 65 5 0.0 1 4 1 66 3 0.0 1 2 1 67 38 0.0 1 3 35 68 64 0.0 1 29 35 69 25 0.0 1 16 9 70 15 0.0 1 6 9 71 7 0.0 1 2 5 72 2 0.0 1 0 2 73 1 0.0 1 1 74 1 0.0 1 0 1 80 1 0.0 1 0 1 87 1 0.0 1 0 1 90 2 0.0 1 2 92 1 0.0 1 1 93 2 0.0 1 2 96 1 0.0 1 0 1 100 1 0.0 1 0 1 101 1 0.0 1 0 1 108 2 0.0 1 1 1 109 1 0.0 1 1 112 1 0.0 1 0 1 113 2 0.0 1 1 1 117 1 0.0 1 1 135 1 0.0 1 0 1 136 1 0.0 1 0 1 140 1 0.0 1 0 1 143 1 0.0 1 1 148 1 0.0 1 0 1 149 1 0.0 1 0 1 150 6 0.0 1 0 6 151 3 0.0 1 0 3 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001.fastq.gz ============================================= 87562 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 87562 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21734 (24.82%)