SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_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-2to4kb-6_S22_L006_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.19 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 256,911 Reads with adapters: 55,558 (21.6%) Reads written (passing filters): 256,911 (100.0%) Total basepairs processed: 30,598,372 bp Quality-trimmed: 4,787,179 bp (15.6%) Total written (filtered): 25,683,113 bp (83.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55558 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 25.3% G: 13.3% T: 30.5% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 41307 64227.8 0 41307 2 10041 16056.9 0 10041 3 2188 4014.2 0 2188 4 915 1003.6 0 915 5 179 250.9 0 179 6 24 62.7 0 24 7 15 15.7 0 15 8 11 3.9 0 11 9 3 1.0 0 1 2 10 14 0.2 1 4 10 11 6 0.1 1 2 4 12 4 0.0 1 2 2 13 1 0.0 1 0 1 14 10 0.0 1 7 3 15 6 0.0 1 4 2 16 1 0.0 1 1 17 8 0.0 1 4 4 18 1 0.0 1 0 1 19 8 0.0 1 5 3 20 4 0.0 1 3 1 21 3 0.0 1 1 2 22 1 0.0 1 1 23 2 0.0 1 1 1 24 16 0.0 1 13 3 25 5 0.0 1 2 3 26 5 0.0 1 1 4 28 4 0.0 1 4 30 7 0.0 1 6 1 31 2 0.0 1 1 1 32 7 0.0 1 5 2 33 10 0.0 1 8 2 34 2 0.0 1 1 1 35 1 0.0 1 1 36 1 0.0 1 1 37 1 0.0 1 1 38 2 0.0 1 1 1 39 6 0.0 1 2 4 40 3 0.0 1 2 1 41 9 0.0 1 5 4 42 9 0.0 1 4 5 43 3 0.0 1 2 1 44 9 0.0 1 8 1 45 13 0.0 1 10 3 46 7 0.0 1 4 3 47 3 0.0 1 1 2 48 7 0.0 1 3 4 49 6 0.0 1 5 1 50 7 0.0 1 5 2 51 18 0.0 1 12 6 52 9 0.0 1 7 2 53 3 0.0 1 2 1 54 2 0.0 1 2 55 5 0.0 1 3 2 56 2 0.0 1 2 57 7 0.0 1 6 1 58 16 0.0 1 15 1 59 10 0.0 1 8 2 60 2 0.0 1 2 61 2 0.0 1 2 62 6 0.0 1 5 1 63 11 0.0 1 10 1 64 2 0.0 1 2 65 14 0.0 1 10 4 66 12 0.0 1 8 4 67 99 0.0 1 12 87 68 180 0.0 1 70 110 69 82 0.0 1 42 40 70 45 0.0 1 12 33 71 14 0.0 1 7 7 72 4 0.0 1 0 4 73 7 0.0 1 3 4 74 3 0.0 1 1 2 75 3 0.0 1 2 1 77 3 0.0 1 2 1 79 4 0.0 1 3 1 80 6 0.0 1 4 2 81 3 0.0 1 1 2 82 4 0.0 1 2 2 83 1 0.0 1 1 84 1 0.0 1 0 1 85 2 0.0 1 0 2 86 2 0.0 1 1 1 87 1 0.0 1 1 88 1 0.0 1 1 90 2 0.0 1 1 1 91 1 0.0 1 0 1 93 2 0.0 1 1 1 94 2 0.0 1 0 2 95 3 0.0 1 2 1 97 1 0.0 1 1 98 2 0.0 1 1 1 100 1 0.0 1 0 1 101 1 0.0 1 1 103 1 0.0 1 1 105 1 0.0 1 1 106 3 0.0 1 2 1 108 2 0.0 1 1 1 109 1 0.0 1 1 110 1 0.0 1 1 111 2 0.0 1 1 1 113 4 0.0 1 3 1 114 1 0.0 1 0 1 118 3 0.0 1 2 1 119 1 0.0 1 0 1 120 2 0.0 1 1 1 121 1 0.0 1 1 123 2 0.0 1 1 1 124 1 0.0 1 0 1 129 1 0.0 1 1 131 2 0.0 1 1 1 134 1 0.0 1 1 146 1 0.0 1 1 148 2 0.0 1 0 2 149 2 0.0 1 0 2 150 19 0.0 1 4 15 151 6 0.0 1 1 5 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001.fastq.gz ============================================= 256911 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 256911 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 59359 (23.10%)