SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_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_6_S5_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 2284.51 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 73,192,078 Reads with adapters: 38,909,941 (53.2%) Reads written (passing filters): 73,192,078 (100.0%) Total basepairs processed: 9,070,248,848 bp Quality-trimmed: 5,447,904 bp (0.1%) Total written (filtered): 9,013,153,573 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38909941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 20.6% G: 14.2% T: 25.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29294615 18298019.5 0 29294615 2 7281849 4574504.9 0 7281849 3 2053808 1143626.2 0 2053808 4 177566 285906.6 0 177566 5 73954 71476.6 0 73954 6 13089 17869.2 0 13089 7 2757 4467.3 0 2757 8 380 1116.8 0 380 9 2284 279.2 0 194 2090 10 2964 69.8 1 61 2903 11 1037 17.5 1 6 1031 12 241 4.4 1 2 239 13 45 1.1 1 0 45 14 45 1.1 1 0 45 15 47 1.1 1 0 47 16 49 1.1 1 0 49 17 39 1.1 1 0 39 18 54 1.1 1 0 54 19 44 1.1 1 1 43 20 57 1.1 1 0 57 21 61 1.1 1 0 61 22 67 1.1 1 1 66 23 60 1.1 1 0 60 24 53 1.1 1 0 53 25 52 1.1 1 0 52 26 33 1.1 1 0 33 27 45 1.1 1 0 45 28 44 1.1 1 0 44 29 100 1.1 1 0 100 30 38 1.1 1 0 38 31 42 1.1 1 0 42 32 62 1.1 1 0 62 33 51 1.1 1 0 51 34 46 1.1 1 0 46 35 69 1.1 1 0 69 36 38 1.1 1 0 38 37 48 1.1 1 0 48 38 38 1.1 1 0 38 39 53 1.1 1 0 53 40 41 1.1 1 0 41 41 59 1.1 1 3 56 42 44 1.1 1 0 44 43 42 1.1 1 0 42 44 43 1.1 1 0 43 45 84 1.1 1 0 84 46 19 1.1 1 0 19 47 33 1.1 1 0 33 48 46 1.1 1 0 46 49 79 1.1 1 0 79 50 43 1.1 1 0 43 51 48 1.1 1 0 48 52 42 1.1 1 0 42 53 24 1.1 1 0 24 54 47 1.1 1 0 47 55 39 1.1 1 0 39 56 31 1.1 1 0 31 57 53 1.1 1 0 53 58 38 1.1 1 0 38 59 44 1.1 1 0 44 60 61 1.1 1 0 61 61 45 1.1 1 0 45 62 51 1.1 1 0 51 63 31 1.1 1 0 31 64 34 1.1 1 0 34 65 61 1.1 1 0 61 66 48 1.1 1 0 48 67 37 1.1 1 0 37 68 42 1.1 1 0 42 69 35 1.1 1 0 35 70 55 1.1 1 0 55 71 41 1.1 1 0 41 72 62 1.1 1 0 62 73 53 1.1 1 0 53 74 29 1.1 1 0 29 75 37 1.1 1 0 37 76 46 1.1 1 0 46 77 48 1.1 1 0 48 78 49 1.1 1 0 49 79 47 1.1 1 0 47 80 19 1.1 1 0 19 81 20 1.1 1 0 20 82 43 1.1 1 0 43 83 42 1.1 1 1 41 84 41 1.1 1 0 41 85 33 1.1 1 0 33 86 62 1.1 1 0 62 87 46 1.1 1 0 46 88 42 1.1 1 0 42 89 39 1.1 1 0 39 90 51 1.1 1 0 51 91 34 1.1 1 0 34 92 44 1.1 1 0 44 93 41 1.1 1 0 41 94 29 1.1 1 0 29 95 29 1.1 1 0 29 96 72 1.1 1 0 72 97 42 1.1 1 0 42 98 34 1.1 1 0 34 99 40 1.1 1 0 40 100 20 1.1 1 0 20 101 62 1.1 1 0 62 102 26 1.1 1 0 26 103 37 1.1 1 0 37 104 29 1.1 1 0 29 105 68 1.1 1 0 68 106 23 1.1 1 0 23 107 52 1.1 1 0 52 108 35 1.1 1 0 35 109 34 1.1 1 0 34 110 24 1.1 1 0 24 111 42 1.1 1 0 42 112 28 1.1 1 0 28 113 39 1.1 1 0 39 114 42 1.1 1 0 42 115 51 1.1 1 0 51 116 43 1.1 1 0 43 117 28 1.1 1 0 28 118 42 1.1 1 0 42 119 30 1.1 1 0 30 120 24 1.1 1 0 24 121 31 1.1 1 0 31 122 32 1.1 1 0 32 123 40 1.1 1 0 40 124 42 1.1 1 0 42 125 22 1.1 1 0 22 126 34 1.1 1 0 34 127 37 1.1 1 0 37 128 28 1.1 1 0 28 129 34 1.1 1 0 34 130 45 1.1 1 0 45 131 38 1.1 1 0 38 132 38 1.1 1 0 38 133 28 1.1 1 0 28 134 12 1.1 1 0 12 135 38 1.1 1 0 38 136 31 1.1 1 0 31 137 29 1.1 1 0 29 138 24 1.1 1 0 24 139 23 1.1 1 0 23 140 13 1.1 1 0 13 141 5 1.1 1 0 5 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz ============================================= 73192078 sequences processed in total