SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_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-7_S26_L007_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 15.61 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 498,123 Reads with adapters: 114,354 (23.0%) Reads written (passing filters): 498,123 (100.0%) Total basepairs processed: 59,164,906 bp Quality-trimmed: 5,701,729 bp (9.6%) Total written (filtered): 53,160,578 bp (89.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 114354 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.8% C: 25.8% G: 14.0% T: 28.8% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 83738 124530.8 0 83738 2 21124 31132.7 0 21124 3 4777 7783.2 0 4777 4 1789 1945.8 0 1789 5 349 486.4 0 349 6 58 121.6 0 58 7 49 30.4 0 49 8 30 7.6 0 30 9 7 1.9 0 5 2 10 20 0.5 1 8 12 11 6 0.1 1 2 4 12 20 0.0 1 10 10 13 7 0.0 1 7 14 35 0.0 1 18 17 15 16 0.0 1 14 2 16 13 0.0 1 8 5 17 38 0.0 1 25 13 18 4 0.0 1 3 1 19 22 0.0 1 14 8 20 19 0.0 1 16 3 21 1 0.0 1 1 22 4 0.0 1 0 4 23 18 0.0 1 10 8 24 37 0.0 1 29 8 25 15 0.0 1 8 7 26 27 0.0 1 17 10 27 5 0.0 1 2 3 28 9 0.0 1 5 4 29 3 0.0 1 3 30 24 0.0 1 17 7 31 1 0.0 1 1 32 16 0.0 1 11 5 33 33 0.0 1 24 9 34 5 0.0 1 2 3 35 14 0.0 1 7 7 36 8 0.0 1 8 37 19 0.0 1 11 8 38 5 0.0 1 5 39 14 0.0 1 13 1 40 3 0.0 1 0 3 41 25 0.0 1 18 7 42 34 0.0 1 27 7 43 6 0.0 1 5 1 44 23 0.0 1 12 11 45 43 0.0 1 35 8 46 14 0.0 1 10 4 47 4 0.0 1 3 1 48 28 0.0 1 21 7 49 16 0.0 1 12 4 50 4 0.0 1 3 1 51 95 0.0 1 71 24 52 10 0.0 1 7 3 53 4 0.0 1 4 54 22 0.0 1 19 3 55 20 0.0 1 17 3 56 11 0.0 1 10 1 57 19 0.0 1 17 2 58 30 0.0 1 23 7 59 24 0.0 1 17 7 60 19 0.0 1 14 5 61 16 0.0 1 13 3 62 23 0.0 1 16 7 63 31 0.0 1 25 6 64 25 0.0 1 21 4 65 19 0.0 1 16 3 66 43 0.0 1 29 14 67 182 0.0 1 32 150 68 407 0.0 1 308 99 69 182 0.0 1 129 53 70 84 0.0 1 55 29 71 34 0.0 1 22 12 72 33 0.0 1 19 14 73 25 0.0 1 19 6 74 16 0.0 1 9 7 75 17 0.0 1 16 1 76 6 0.0 1 1 5 77 10 0.0 1 8 2 78 8 0.0 1 5 3 79 14 0.0 1 10 4 80 11 0.0 1 10 1 81 8 0.0 1 3 5 82 7 0.0 1 6 1 83 6 0.0 1 6 84 10 0.0 1 5 5 85 7 0.0 1 3 4 86 8 0.0 1 8 87 7 0.0 1 4 3 88 6 0.0 1 4 2 89 7 0.0 1 5 2 90 7 0.0 1 4 3 91 12 0.0 1 8 4 92 9 0.0 1 5 4 93 2 0.0 1 2 94 5 0.0 1 2 3 95 4 0.0 1 3 1 96 6 0.0 1 3 3 97 9 0.0 1 6 3 98 8 0.0 1 6 2 99 6 0.0 1 4 2 100 5 0.0 1 4 1 101 3 0.0 1 2 1 102 9 0.0 1 6 3 103 6 0.0 1 4 2 104 4 0.0 1 3 1 105 2 0.0 1 1 1 106 10 0.0 1 8 2 107 5 0.0 1 1 4 108 2 0.0 1 1 1 109 8 0.0 1 4 4 110 7 0.0 1 4 3 111 5 0.0 1 4 1 112 6 0.0 1 6 113 1 0.0 1 1 114 9 0.0 1 6 3 115 5 0.0 1 4 1 116 5 0.0 1 3 2 119 2 0.0 1 1 1 120 1 0.0 1 0 1 121 3 0.0 1 2 1 122 1 0.0 1 0 1 124 5 0.0 1 3 2 125 2 0.0 1 1 1 126 7 0.0 1 6 1 127 2 0.0 1 1 1 128 1 0.0 1 1 129 1 0.0 1 1 130 1 0.0 1 1 138 1 0.0 1 0 1 144 2 0.0 1 0 2 145 2 0.0 1 0 2 146 2 0.0 1 0 2 148 2 0.0 1 0 2 149 12 0.0 1 4 8 150 54 0.0 1 18 36 151 8 0.0 1 1 7 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001.fastq.gz ============================================= 498123 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 498123 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 119990 (24.09%)