SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_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-2to4kb-6_S22_L006_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9.20 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 256,911 Reads with adapters: 64,054 (24.9%) Reads written (passing filters): 256,911 (100.0%) Total basepairs processed: 32,102,933 bp Quality-trimmed: 1,174,253 bp (3.7%) Total written (filtered): 30,796,322 bp (95.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64054 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.0% C: 22.9% G: 13.3% T: 28.2% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 49428 64227.8 0 49428 2 10009 16056.9 0 10009 3 2799 4014.2 0 2799 4 949 1003.6 0 949 5 204 250.9 0 204 6 20 62.7 0 20 7 10 15.7 0 10 8 3 3.9 0 3 9 3 1.0 0 3 10 10 0.2 1 3 7 11 2 0.1 1 0 2 12 2 0.0 1 1 1 13 4 0.0 1 3 1 14 3 0.0 1 2 1 15 4 0.0 1 3 1 16 2 0.0 1 2 18 4 0.0 1 3 1 19 5 0.0 1 3 2 20 1 0.0 1 0 1 22 6 0.0 1 1 5 23 5 0.0 1 3 2 24 6 0.0 1 5 1 25 1 0.0 1 0 1 26 1 0.0 1 1 27 2 0.0 1 0 2 28 4 0.0 1 2 2 30 3 0.0 1 1 2 31 3 0.0 1 2 1 32 4 0.0 1 3 1 33 2 0.0 1 2 34 1 0.0 1 0 1 35 3 0.0 1 1 2 36 2 0.0 1 1 1 38 3 0.0 1 2 1 39 3 0.0 1 3 41 7 0.0 1 3 4 42 3 0.0 1 3 43 2 0.0 1 1 1 44 3 0.0 1 1 2 45 4 0.0 1 2 2 46 1 0.0 1 1 49 1 0.0 1 1 50 3 0.0 1 2 1 51 1 0.0 1 1 52 1 0.0 1 0 1 53 2 0.0 1 2 54 2 0.0 1 0 2 55 5 0.0 1 4 1 56 7 0.0 1 6 1 57 5 0.0 1 4 1 58 1 0.0 1 1 59 4 0.0 1 4 60 1 0.0 1 1 61 1 0.0 1 1 62 1 0.0 1 1 63 2 0.0 1 2 65 1 0.0 1 1 66 4 0.0 1 4 67 4 0.0 1 4 68 1 0.0 1 0 1 69 2 0.0 1 2 70 4 0.0 1 3 1 71 2 0.0 1 2 72 7 0.0 1 6 1 73 4 0.0 1 3 1 74 9 0.0 1 5 4 75 77 0.0 1 8 69 76 87 0.0 1 37 50 77 58 0.0 1 25 33 78 30 0.0 1 15 15 79 18 0.0 1 3 15 80 12 0.0 1 4 8 81 9 0.0 1 3 6 82 7 0.0 1 2 5 83 6 0.0 1 5 1 84 4 0.0 1 2 2 85 3 0.0 1 1 2 86 3 0.0 1 1 2 87 4 0.0 1 2 2 88 1 0.0 1 1 89 3 0.0 1 0 3 90 5 0.0 1 2 3 93 2 0.0 1 1 1 94 2 0.0 1 2 95 1 0.0 1 0 1 97 1 0.0 1 0 1 98 1 0.0 1 0 1 101 2 0.0 1 1 1 102 3 0.0 1 1 2 103 2 0.0 1 0 2 104 1 0.0 1 1 106 3 0.0 1 3 107 1 0.0 1 0 1 108 1 0.0 1 0 1 109 2 0.0 1 0 2 110 1 0.0 1 0 1 114 1 0.0 1 0 1 115 1 0.0 1 1 117 1 0.0 1 0 1 118 2 0.0 1 2 119 1 0.0 1 1 121 1 0.0 1 0 1 122 2 0.0 1 0 2 124 1 0.0 1 1 129 1 0.0 1 0 1 130 2 0.0 1 1 1 131 1 0.0 1 0 1 132 1 0.0 1 0 1 134 1 0.0 1 1 135 2 0.0 1 2 137 1 0.0 1 0 1 138 1 0.0 1 0 1 141 1 0.0 1 1 142 1 0.0 1 0 1 145 1 0.0 1 0 1 147 4 0.0 1 0 4 148 5 0.0 1 0 5 149 14 0.0 1 1 13 150 39 0.0 1 7 32 151 13 0.0 1 2 11 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001.fastq.gz ============================================= 256911 sequences processed in total