SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.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_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2398.35 s (33 us/read; 1.83 M reads/minute). === Summary === Total reads processed: 73,192,078 Reads with adapters: 26,780,011 (36.6%) Reads written (passing filters): 73,192,078 (100.0%) Total basepairs processed: 8,814,341,687 bp Quality-trimmed: 19,241,904 bp (0.2%) Total written (filtered): 8,764,670,030 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26780011 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.0% C: 21.3% G: 5.2% T: 25.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24336596 18298019.5 0 24336596 2 1776956 4574504.9 0 1776956 3 497249 1143626.2 0 497249 4 154272 285906.6 0 154272 5 4282 71476.6 0 4282 6 2808 17869.2 0 2808 7 676 4467.3 0 676 8 109 1116.8 0 109 9 654 279.2 0 195 459 10 751 69.8 1 8 743 11 306 17.5 1 3 303 12 123 4.4 1 0 123 13 34 1.1 1 0 34 14 57 1.1 1 0 57 15 40 1.1 1 1 39 16 35 1.1 1 1 34 17 49 1.1 1 1 48 18 56 1.1 1 0 56 19 59 1.1 1 0 59 20 43 1.1 1 0 43 21 49 1.1 1 0 49 22 65 1.1 1 0 65 23 46 1.1 1 0 46 24 41 1.1 1 0 41 25 62 1.1 1 0 62 26 64 1.1 1 0 64 27 46 1.1 1 0 46 28 95 1.1 1 0 95 29 25 1.1 1 0 25 30 53 1.1 1 0 53 31 34 1.1 1 0 34 32 39 1.1 1 0 39 33 54 1.1 1 1 53 34 41 1.1 1 1 40 35 62 1.1 1 0 62 36 39 1.1 1 0 39 37 37 1.1 1 0 37 38 55 1.1 1 0 55 39 56 1.1 1 0 56 40 40 1.1 1 0 40 41 51 1.1 1 0 51 42 30 1.1 1 0 30 43 54 1.1 1 0 54 44 38 1.1 1 0 38 45 55 1.1 1 0 55 46 72 1.1 1 0 72 47 52 1.1 1 0 52 48 32 1.1 1 0 32 49 42 1.1 1 0 42 50 42 1.1 1 0 42 51 41 1.1 1 0 41 52 30 1.1 1 1 29 53 32 1.1 1 2 30 54 32 1.1 1 0 32 55 29 1.1 1 0 29 56 45 1.1 1 0 45 57 27 1.1 1 0 27 58 33 1.1 1 0 33 59 34 1.1 1 1 33 60 47 1.1 1 0 47 61 74 1.1 1 0 74 62 46 1.1 1 0 46 63 55 1.1 1 2 53 64 37 1.1 1 0 37 65 31 1.1 1 0 31 66 59 1.1 1 0 59 67 42 1.1 1 0 42 68 38 1.1 1 0 38 69 42 1.1 1 0 42 70 53 1.1 1 0 53 71 61 1.1 1 0 61 72 73 1.1 1 0 73 73 47 1.1 1 0 47 74 43 1.1 1 0 43 75 34 1.1 1 0 34 76 32 1.1 1 0 32 77 39 1.1 1 0 39 78 53 1.1 1 0 53 79 37 1.1 1 0 37 80 50 1.1 1 0 50 81 34 1.1 1 0 34 82 35 1.1 1 0 35 83 38 1.1 1 0 38 84 35 1.1 1 0 35 85 42 1.1 1 0 42 86 35 1.1 1 1 34 87 36 1.1 1 0 36 88 38 1.1 1 0 38 89 51 1.1 1 0 51 90 40 1.1 1 0 40 91 44 1.1 1 0 44 92 35 1.1 1 0 35 93 37 1.1 1 0 37 94 65 1.1 1 0 65 95 53 1.1 1 0 53 96 41 1.1 1 0 41 97 44 1.1 1 0 44 98 39 1.1 1 0 39 99 40 1.1 1 0 40 100 35 1.1 1 0 35 101 32 1.1 1 0 32 102 41 1.1 1 0 41 103 68 1.1 1 0 68 104 56 1.1 1 0 56 105 18 1.1 1 0 18 106 42 1.1 1 0 42 107 42 1.1 1 0 42 108 25 1.1 1 0 25 109 29 1.1 1 0 29 110 25 1.1 1 0 25 111 31 1.1 1 0 31 112 35 1.1 1 0 35 113 39 1.1 1 0 39 114 29 1.1 1 0 29 115 34 1.1 1 0 34 116 48 1.1 1 0 48 117 39 1.1 1 0 39 118 27 1.1 1 0 27 119 26 1.1 1 0 26 120 38 1.1 1 0 38 121 34 1.1 1 3 31 122 32 1.1 1 0 32 123 27 1.1 1 0 27 124 33 1.1 1 0 33 125 18 1.1 1 0 18 126 37 1.1 1 0 37 127 44 1.1 1 0 44 128 43 1.1 1 0 43 129 21 1.1 1 0 21 130 33 1.1 1 0 33 131 31 1.1 1 0 31 132 29 1.1 1 0 29 133 27 1.1 1 0 27 134 27 1.1 1 0 27 135 25 1.1 1 0 25 136 17 1.1 1 0 17 137 22 1.1 1 0 22 138 16 1.1 1 0 16 139 17 1.1 1 0 17 140 6 1.1 1 0 6 141 9 1.1 1 0 9 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz ============================================= 73192078 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73192078 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1330834 (1.82%)