SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_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 2844.06 s (32 us/read; 1.85 M reads/minute). === Summary === Total reads processed: 87,796,904 Reads with adapters: 32,159,143 (36.6%) Reads written (passing filters): 87,796,904 (100.0%) Total basepairs processed: 10,520,390,091 bp Quality-trimmed: 21,808,749 bp (0.2%) Total written (filtered): 10,462,140,160 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32159143 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.4% C: 20.9% G: 5.1% T: 25.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29258517 21949226.0 0 29258517 2 2105430 5487306.5 0 2105430 3 590395 1371826.6 0 590395 4 188733 342956.7 0 188733 5 4513 85739.2 0 4513 6 3281 21434.8 0 3281 7 804 5358.7 0 804 8 140 1339.7 0 140 9 687 334.9 0 212 475 10 782 83.7 1 14 768 11 315 20.9 1 1 314 12 118 5.2 1 0 118 13 32 1.3 1 0 32 14 55 1.3 1 0 55 15 38 1.3 1 0 38 16 42 1.3 1 0 42 17 35 1.3 1 0 35 18 67 1.3 1 0 67 19 58 1.3 1 0 58 20 57 1.3 1 0 57 21 47 1.3 1 0 47 22 62 1.3 1 0 62 23 72 1.3 1 0 72 24 59 1.3 1 2 57 25 79 1.3 1 0 79 26 54 1.3 1 0 54 27 42 1.3 1 0 42 28 55 1.3 1 0 55 29 44 1.3 1 0 44 30 47 1.3 1 1 46 31 44 1.3 1 0 44 32 41 1.3 1 0 41 33 60 1.3 1 0 60 34 54 1.3 1 0 54 35 48 1.3 1 0 48 36 59 1.3 1 0 59 37 55 1.3 1 0 55 38 57 1.3 1 0 57 39 64 1.3 1 0 64 40 39 1.3 1 0 39 41 57 1.3 1 0 57 42 43 1.3 1 0 43 43 54 1.3 1 0 54 44 48 1.3 1 0 48 45 41 1.3 1 0 41 46 53 1.3 1 0 53 47 35 1.3 1 0 35 48 54 1.3 1 0 54 49 42 1.3 1 0 42 50 92 1.3 1 0 92 51 49 1.3 1 0 49 52 52 1.3 1 0 52 53 65 1.3 1 0 65 54 36 1.3 1 0 36 55 46 1.3 1 0 46 56 50 1.3 1 0 50 57 38 1.3 1 1 37 58 32 1.3 1 0 32 59 42 1.3 1 0 42 60 41 1.3 1 0 41 61 50 1.3 1 0 50 62 38 1.3 1 0 38 63 52 1.3 1 0 52 64 41 1.3 1 0 41 65 34 1.3 1 0 34 66 38 1.3 1 0 38 67 36 1.3 1 0 36 68 51 1.3 1 0 51 69 40 1.3 1 0 40 70 42 1.3 1 0 42 71 51 1.3 1 0 51 72 47 1.3 1 0 47 73 39 1.3 1 0 39 74 41 1.3 1 0 41 75 41 1.3 1 0 41 76 41 1.3 1 0 41 77 40 1.3 1 0 40 78 45 1.3 1 1 44 79 34 1.3 1 0 34 80 41 1.3 1 0 41 81 42 1.3 1 0 42 82 43 1.3 1 0 43 83 53 1.3 1 0 53 84 46 1.3 1 0 46 85 29 1.3 1 1 28 86 50 1.3 1 0 50 87 42 1.3 1 0 42 88 46 1.3 1 0 46 89 44 1.3 1 0 44 90 23 1.3 1 0 23 91 50 1.3 1 1 49 92 28 1.3 1 0 28 93 33 1.3 1 0 33 94 68 1.3 1 0 68 95 47 1.3 1 0 47 96 30 1.3 1 0 30 97 48 1.3 1 0 48 98 57 1.3 1 0 57 99 49 1.3 1 0 49 100 37 1.3 1 0 37 101 27 1.3 1 0 27 102 33 1.3 1 0 33 103 48 1.3 1 0 48 104 47 1.3 1 0 47 105 30 1.3 1 0 30 106 33 1.3 1 0 33 107 36 1.3 1 0 36 108 47 1.3 1 0 47 109 46 1.3 1 0 46 110 17 1.3 1 0 17 111 30 1.3 1 0 30 112 30 1.3 1 0 30 113 47 1.3 1 0 47 114 39 1.3 1 0 39 115 41 1.3 1 0 41 116 54 1.3 1 0 54 117 27 1.3 1 0 27 118 32 1.3 1 0 32 119 27 1.3 1 0 27 120 46 1.3 1 0 46 121 28 1.3 1 0 28 122 44 1.3 1 0 44 123 27 1.3 1 0 27 124 37 1.3 1 0 37 125 25 1.3 1 0 25 126 25 1.3 1 0 25 127 30 1.3 1 0 30 128 34 1.3 1 3 31 129 43 1.3 1 0 43 130 33 1.3 1 0 33 131 36 1.3 1 0 36 132 25 1.3 1 0 25 133 19 1.3 1 0 19 134 13 1.3 1 0 13 135 34 1.3 1 0 34 136 36 1.3 1 0 36 137 15 1.3 1 0 15 138 11 1.3 1 0 11 139 18 1.3 1 0 18 140 3 1.3 1 0 3 141 12 1.3 1 0 12 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz ============================================= 87796904 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 87796904 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1630281 (1.86%)