SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_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_2_S4_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 2533.76 s (31 us/read; 1.94 M reads/minute). === Summary === Total reads processed: 81,915,909 Reads with adapters: 43,086,020 (52.6%) Reads written (passing filters): 81,915,909 (100.0%) Total basepairs processed: 10,082,741,867 bp Quality-trimmed: 6,642,171 bp (0.1%) Total written (filtered): 10,019,067,706 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43086020 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.1% C: 20.7% G: 14.6% T: 25.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32531578 20478977.2 0 32531578 2 7993009 5119744.3 0 7993009 3 2259950 1279936.1 0 2259950 4 196255 319984.0 0 196255 5 75854 79996.0 0 75854 6 13495 19999.0 0 13495 7 2651 4999.8 0 2651 8 474 1249.9 0 474 9 2451 312.5 0 148 2303 10 3328 78.1 1 45 3283 11 1135 19.5 1 8 1127 12 289 4.9 1 1 288 13 58 1.2 1 0 58 14 40 1.2 1 0 40 15 51 1.2 1 0 51 16 38 1.2 1 1 37 17 42 1.2 1 0 42 18 63 1.2 1 0 63 19 54 1.2 1 0 54 20 41 1.2 1 1 40 21 63 1.2 1 0 63 22 57 1.2 1 0 57 23 69 1.2 1 1 68 24 60 1.2 1 0 60 25 55 1.2 1 0 55 26 55 1.2 1 0 55 27 51 1.2 1 0 51 28 46 1.2 1 0 46 29 74 1.2 1 0 74 30 40 1.2 1 0 40 31 45 1.2 1 0 45 32 49 1.2 1 0 49 33 50 1.2 1 0 50 34 45 1.2 1 0 45 35 66 1.2 1 0 66 36 43 1.2 1 0 43 37 51 1.2 1 0 51 38 49 1.2 1 0 49 39 55 1.2 1 0 55 40 53 1.2 1 0 53 41 47 1.2 1 0 47 42 38 1.2 1 0 38 43 36 1.2 1 0 36 44 47 1.2 1 1 46 45 80 1.2 1 0 80 46 46 1.2 1 0 46 47 53 1.2 1 0 53 48 41 1.2 1 0 41 49 69 1.2 1 0 69 50 31 1.2 1 0 31 51 47 1.2 1 0 47 52 51 1.2 1 0 51 53 41 1.2 1 0 41 54 49 1.2 1 0 49 55 37 1.2 1 0 37 56 25 1.2 1 0 25 57 50 1.2 1 0 50 58 30 1.2 1 0 30 59 41 1.2 1 0 41 60 45 1.2 1 0 45 61 39 1.2 1 0 39 62 45 1.2 1 0 45 63 52 1.2 1 0 52 64 32 1.2 1 0 32 65 49 1.2 1 0 49 66 42 1.2 1 0 42 67 32 1.2 1 0 32 68 34 1.2 1 0 34 69 60 1.2 1 2 58 70 49 1.2 1 0 49 71 63 1.2 1 0 63 72 47 1.2 1 0 47 73 33 1.2 1 0 33 74 36 1.2 1 0 36 75 39 1.2 1 0 39 76 48 1.2 1 0 48 77 41 1.2 1 0 41 78 42 1.2 1 0 42 79 65 1.2 1 0 65 80 38 1.2 1 0 38 81 20 1.2 1 0 20 82 56 1.2 1 0 56 83 39 1.2 1 0 39 84 38 1.2 1 0 38 85 57 1.2 1 0 57 86 46 1.2 1 0 46 87 54 1.2 1 0 54 88 37 1.2 1 0 37 89 18 1.2 1 0 18 90 44 1.2 1 0 44 91 50 1.2 1 0 50 92 47 1.2 1 0 47 93 67 1.2 1 0 67 94 40 1.2 1 1 39 95 46 1.2 1 0 46 96 57 1.2 1 1 56 97 39 1.2 1 0 39 98 20 1.2 1 0 20 99 41 1.2 1 0 41 100 28 1.2 1 0 28 101 31 1.2 1 0 31 102 52 1.2 1 0 52 103 54 1.2 1 2 52 104 46 1.2 1 1 45 105 60 1.2 1 0 60 106 25 1.2 1 0 25 107 43 1.2 1 0 43 108 28 1.2 1 0 28 109 35 1.2 1 0 35 110 29 1.2 1 0 29 111 44 1.2 1 0 44 112 37 1.2 1 0 37 113 41 1.2 1 0 41 114 46 1.2 1 0 46 115 42 1.2 1 1 41 116 34 1.2 1 2 32 117 47 1.2 1 0 47 118 58 1.2 1 0 58 119 50 1.2 1 0 50 120 51 1.2 1 0 51 121 37 1.2 1 0 37 122 30 1.2 1 0 30 123 30 1.2 1 0 30 124 22 1.2 1 0 22 125 24 1.2 1 0 24 126 39 1.2 1 0 39 127 32 1.2 1 0 32 128 30 1.2 1 0 30 129 41 1.2 1 0 41 130 29 1.2 1 0 29 131 33 1.2 1 0 33 132 30 1.2 1 0 30 133 38 1.2 1 0 38 134 20 1.2 1 0 20 135 35 1.2 1 0 35 136 25 1.2 1 0 25 137 29 1.2 1 0 29 138 27 1.2 1 0 27 139 18 1.2 1 0 18 140 24 1.2 1 0 24 141 8 1.2 1 0 8 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz ============================================= 81915909 sequences processed in total