SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.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; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2228.49 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 71,733,777 Reads with adapters: 39,189,986 (54.6%) Reads written (passing filters): 71,733,777 (100.0%) Total basepairs processed: 8,977,160,164 bp Quality-trimmed: 5,550,572 bp (0.1%) Total written (filtered): 8,920,153,289 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39189986 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 20.1% G: 13.9% T: 26.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29988597 17933444.2 0 29988597 2 6858970 4483361.1 0 6858970 3 2069436 1120840.3 0 2069436 4 184402 280210.1 0 184402 5 64402 70052.5 0 64402 6 10720 17513.1 0 10720 7 2103 4378.3 0 2103 8 386 1094.6 0 386 9 2129 273.6 0 152 1977 10 2889 68.4 1 34 2855 11 959 17.1 1 4 955 12 247 4.3 1 0 247 13 53 1.1 1 0 53 14 32 1.1 1 0 32 15 34 1.1 1 0 34 16 29 1.1 1 0 29 17 29 1.1 1 0 29 18 52 1.1 1 2 50 19 42 1.1 1 0 42 20 51 1.1 1 0 51 21 74 1.1 1 0 74 22 54 1.1 1 0 54 23 70 1.1 1 0 70 24 51 1.1 1 0 51 25 46 1.1 1 0 46 26 38 1.1 1 0 38 27 41 1.1 1 0 41 28 43 1.1 1 0 43 29 83 1.1 1 0 83 30 31 1.1 1 0 31 31 41 1.1 1 0 41 32 39 1.1 1 0 39 33 33 1.1 1 0 33 34 51 1.1 1 0 51 35 55 1.1 1 0 55 36 28 1.1 1 0 28 37 31 1.1 1 0 31 38 38 1.1 1 0 38 39 34 1.1 1 0 34 40 29 1.1 1 0 29 41 40 1.1 1 0 40 42 32 1.1 1 0 32 43 32 1.1 1 0 32 44 23 1.1 1 0 23 45 70 1.1 1 0 70 46 35 1.1 1 0 35 47 49 1.1 1 0 49 48 37 1.1 1 0 37 49 73 1.1 1 0 73 50 29 1.1 1 0 29 51 21 1.1 1 0 21 52 33 1.1 1 0 33 53 40 1.1 1 0 40 54 26 1.1 1 0 26 55 47 1.1 1 0 47 56 43 1.1 1 0 43 57 43 1.1 1 0 43 58 40 1.1 1 0 40 59 33 1.1 1 1 32 60 42 1.1 1 0 42 61 24 1.1 1 0 24 62 39 1.1 1 0 39 63 40 1.1 1 0 40 64 34 1.1 1 0 34 65 50 1.1 1 0 50 66 25 1.1 1 0 25 67 30 1.1 1 0 30 68 22 1.1 1 0 22 69 45 1.1 1 0 45 70 49 1.1 1 0 49 71 41 1.1 1 0 41 72 57 1.1 1 0 57 73 34 1.1 1 0 34 74 19 1.1 1 0 19 75 41 1.1 1 0 41 76 39 1.1 1 0 39 77 36 1.1 1 2 34 78 41 1.1 1 0 41 79 54 1.1 1 0 54 80 65 1.1 1 0 65 81 18 1.1 1 0 18 82 43 1.1 1 2 41 83 33 1.1 1 0 33 84 33 1.1 1 0 33 85 41 1.1 1 0 41 86 46 1.1 1 0 46 87 44 1.1 1 0 44 88 44 1.1 1 0 44 89 27 1.1 1 0 27 90 30 1.1 1 0 30 91 38 1.1 1 0 38 92 31 1.1 1 0 31 93 61 1.1 1 0 61 94 40 1.1 1 0 40 95 28 1.1 1 0 28 96 46 1.1 1 0 46 97 38 1.1 1 0 38 98 18 1.1 1 0 18 99 40 1.1 1 0 40 100 35 1.1 1 1 34 101 29 1.1 1 0 29 102 42 1.1 1 0 42 103 24 1.1 1 0 24 104 34 1.1 1 0 34 105 48 1.1 1 0 48 106 16 1.1 1 0 16 107 45 1.1 1 0 45 108 35 1.1 1 0 35 109 30 1.1 1 0 30 110 18 1.1 1 0 18 111 43 1.1 1 0 43 112 32 1.1 1 0 32 113 44 1.1 1 0 44 114 29 1.1 1 0 29 115 32 1.1 1 0 32 116 35 1.1 1 0 35 117 29 1.1 1 0 29 118 35 1.1 1 0 35 119 56 1.1 1 0 56 120 27 1.1 1 0 27 121 26 1.1 1 0 26 122 25 1.1 1 0 25 123 48 1.1 1 0 48 124 18 1.1 1 0 18 125 18 1.1 1 0 18 126 23 1.1 1 0 23 127 23 1.1 1 0 23 128 37 1.1 1 0 37 129 35 1.1 1 0 35 130 12 1.1 1 0 12 131 32 1.1 1 0 32 132 22 1.1 1 0 22 133 14 1.1 1 0 14 134 21 1.1 1 0 21 135 46 1.1 1 0 46 136 28 1.1 1 0 28 137 20 1.1 1 0 20 138 28 1.1 1 0 28 139 10 1.1 1 0 10 140 28 1.1 1 0 28 141 10 1.1 1 0 10 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz ============================================= 71733777 sequences processed in total