SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_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 2698.58 s (31 us/read; 1.95 M reads/minute). === Summary === Total reads processed: 87,796,904 Reads with adapters: 46,651,194 (53.1%) Reads written (passing filters): 87,796,904 (100.0%) Total basepairs processed: 10,805,650,041 bp Quality-trimmed: 6,308,354 bp (0.1%) Total written (filtered): 10,737,578,830 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46651194 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 20.3% G: 14.1% T: 25.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 35252729 21949226.0 0 35252729 2 8581491 5487306.5 0 8581491 3 2476883 1371826.6 0 2476883 4 218934 342956.7 0 218934 5 89680 85739.2 0 89680 6 14438 21434.8 0 14438 7 3010 5358.7 0 3010 8 485 1339.7 0 485 9 2660 334.9 0 174 2486 10 3700 83.7 1 62 3638 11 1225 20.9 1 15 1210 12 279 5.2 1 1 278 13 62 1.3 1 0 62 14 51 1.3 1 0 51 15 48 1.3 1 0 48 16 34 1.3 1 0 34 17 48 1.3 1 0 48 18 55 1.3 1 0 55 19 45 1.3 1 0 45 20 52 1.3 1 0 52 21 72 1.3 1 0 72 22 89 1.3 1 0 89 23 54 1.3 1 0 54 24 41 1.3 1 0 41 25 35 1.3 1 0 35 26 42 1.3 1 0 42 27 57 1.3 1 0 57 28 43 1.3 1 0 43 29 82 1.3 1 0 82 30 62 1.3 1 0 62 31 48 1.3 1 0 48 32 61 1.3 1 0 61 33 44 1.3 1 0 44 34 60 1.3 1 0 60 35 57 1.3 1 0 57 36 61 1.3 1 0 61 37 47 1.3 1 1 46 38 52 1.3 1 0 52 39 52 1.3 1 0 52 40 54 1.3 1 1 53 41 42 1.3 1 0 42 42 43 1.3 1 0 43 43 31 1.3 1 2 29 44 55 1.3 1 0 55 45 70 1.3 1 0 70 46 33 1.3 1 0 33 47 48 1.3 1 0 48 48 55 1.3 1 2 53 49 53 1.3 1 0 53 50 49 1.3 1 0 49 51 27 1.3 1 0 27 52 50 1.3 1 0 50 53 38 1.3 1 0 38 54 40 1.3 1 0 40 55 51 1.3 1 0 51 56 36 1.3 1 0 36 57 40 1.3 1 0 40 58 56 1.3 1 1 55 59 47 1.3 1 0 47 60 28 1.3 1 0 28 61 39 1.3 1 0 39 62 71 1.3 1 3 68 63 56 1.3 1 0 56 64 55 1.3 1 0 55 65 50 1.3 1 0 50 66 31 1.3 1 0 31 67 35 1.3 1 0 35 68 48 1.3 1 0 48 69 45 1.3 1 0 45 70 48 1.3 1 0 48 71 50 1.3 1 0 50 72 61 1.3 1 0 61 73 57 1.3 1 0 57 74 19 1.3 1 0 19 75 61 1.3 1 0 61 76 56 1.3 1 2 54 77 48 1.3 1 0 48 78 36 1.3 1 0 36 79 65 1.3 1 0 65 80 36 1.3 1 0 36 81 32 1.3 1 0 32 82 52 1.3 1 0 52 83 34 1.3 1 0 34 84 51 1.3 1 0 51 85 80 1.3 1 0 80 86 60 1.3 1 0 60 87 62 1.3 1 0 62 88 31 1.3 1 0 31 89 41 1.3 1 0 41 90 37 1.3 1 0 37 91 33 1.3 1 0 33 92 37 1.3 1 0 37 93 36 1.3 1 0 36 94 26 1.3 1 0 26 95 24 1.3 1 0 24 96 54 1.3 1 0 54 97 48 1.3 1 0 48 98 34 1.3 1 0 34 99 48 1.3 1 0 48 100 41 1.3 1 0 41 101 45 1.3 1 0 45 102 35 1.3 1 0 35 103 32 1.3 1 0 32 104 42 1.3 1 0 42 105 48 1.3 1 0 48 106 40 1.3 1 0 40 107 57 1.3 1 0 57 108 53 1.3 1 0 53 109 33 1.3 1 0 33 110 23 1.3 1 0 23 111 39 1.3 1 0 39 112 60 1.3 1 0 60 113 58 1.3 1 0 58 114 47 1.3 1 0 47 115 27 1.3 1 0 27 116 51 1.3 1 0 51 117 28 1.3 1 0 28 118 20 1.3 1 0 20 119 35 1.3 1 0 35 120 22 1.3 1 0 22 121 47 1.3 1 0 47 122 33 1.3 1 0 33 123 55 1.3 1 0 55 124 24 1.3 1 0 24 125 17 1.3 1 0 17 126 46 1.3 1 0 46 127 33 1.3 1 0 33 128 45 1.3 1 0 45 129 30 1.3 1 0 30 130 46 1.3 1 0 46 131 44 1.3 1 0 44 132 46 1.3 1 0 46 133 30 1.3 1 0 30 134 16 1.3 1 0 16 135 43 1.3 1 0 43 136 23 1.3 1 0 23 137 30 1.3 1 0 30 138 23 1.3 1 0 23 139 6 1.3 1 0 6 140 13 1.3 1 0 13 141 7 1.3 1 0 7 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz ============================================= 87796904 sequences processed in total