SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_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_5_S6_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 2350.16 s (33 us/read; 1.83 M reads/minute). === Summary === Total reads processed: 71,733,777 Reads with adapters: 26,952,904 (37.6%) Reads written (passing filters): 71,733,777 (100.0%) Total basepairs processed: 8,728,992,125 bp Quality-trimmed: 19,201,281 bp (0.2%) Total written (filtered): 8,679,330,386 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26952904 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.5% C: 20.6% G: 5.1% T: 25.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24590621 17933444.2 0 24590621 2 1716070 4483361.1 0 1716070 3 476291 1120840.3 0 476291 4 157132 280210.1 0 157132 5 3490 70052.5 0 3490 6 2281 17513.1 0 2281 7 598 4378.3 0 598 8 114 1094.6 0 114 9 559 273.6 0 141 418 10 703 68.4 1 12 691 11 238 17.1 1 0 238 12 85 4.3 1 0 85 13 43 1.1 1 0 43 14 42 1.1 1 0 42 15 36 1.1 1 0 36 16 34 1.1 1 0 34 17 41 1.1 1 0 41 18 69 1.1 1 0 69 19 50 1.1 1 0 50 20 35 1.1 1 0 35 21 53 1.1 1 0 53 22 47 1.1 1 1 46 23 59 1.1 1 0 59 24 40 1.1 1 1 39 25 55 1.1 1 0 55 26 48 1.1 1 0 48 27 34 1.1 1 0 34 28 70 1.1 1 0 70 29 46 1.1 1 0 46 30 46 1.1 1 0 46 31 33 1.1 1 0 33 32 47 1.1 1 1 46 33 37 1.1 1 0 37 34 50 1.1 1 0 50 35 64 1.1 1 1 63 36 37 1.1 1 0 37 37 32 1.1 1 0 32 38 43 1.1 1 0 43 39 54 1.1 1 0 54 40 60 1.1 1 0 60 41 46 1.1 1 0 46 42 39 1.1 1 0 39 43 65 1.1 1 0 65 44 28 1.1 1 0 28 45 40 1.1 1 0 40 46 44 1.1 1 0 44 47 44 1.1 1 0 44 48 34 1.1 1 0 34 49 55 1.1 1 0 55 50 45 1.1 1 0 45 51 50 1.1 1 0 50 52 27 1.1 1 0 27 53 47 1.1 1 0 47 54 25 1.1 1 0 25 55 38 1.1 1 0 38 56 49 1.1 1 0 49 57 40 1.1 1 1 39 58 26 1.1 1 0 26 59 42 1.1 1 0 42 60 37 1.1 1 0 37 61 35 1.1 1 0 35 62 37 1.1 1 0 37 63 49 1.1 1 0 49 64 49 1.1 1 0 49 65 31 1.1 1 0 31 66 30 1.1 1 0 30 67 25 1.1 1 0 25 68 38 1.1 1 0 38 69 22 1.1 1 0 22 70 48 1.1 1 0 48 71 52 1.1 1 0 52 72 37 1.1 1 0 37 73 50 1.1 1 0 50 74 37 1.1 1 0 37 75 34 1.1 1 0 34 76 33 1.1 1 0 33 77 33 1.1 1 0 33 78 23 1.1 1 0 23 79 45 1.1 1 0 45 80 49 1.1 1 0 49 81 34 1.1 1 0 34 82 21 1.1 1 0 21 83 28 1.1 1 0 28 84 35 1.1 1 0 35 85 21 1.1 1 0 21 86 46 1.1 1 0 46 87 40 1.1 1 0 40 88 28 1.1 1 0 28 89 29 1.1 1 0 29 90 46 1.1 1 0 46 91 47 1.1 1 0 47 92 29 1.1 1 0 29 93 47 1.1 1 0 47 94 31 1.1 1 0 31 95 27 1.1 1 0 27 96 37 1.1 1 0 37 97 46 1.1 1 0 46 98 19 1.1 1 0 19 99 29 1.1 1 0 29 100 36 1.1 1 0 36 101 32 1.1 1 0 32 102 41 1.1 1 0 41 103 49 1.1 1 0 49 104 28 1.1 1 0 28 105 30 1.1 1 0 30 106 46 1.1 1 0 46 107 33 1.1 1 0 33 108 33 1.1 1 0 33 109 35 1.1 1 0 35 110 19 1.1 1 0 19 111 22 1.1 1 0 22 112 30 1.1 1 0 30 113 38 1.1 1 0 38 114 39 1.1 1 0 39 115 40 1.1 1 0 40 116 35 1.1 1 0 35 117 22 1.1 1 0 22 118 27 1.1 1 0 27 119 31 1.1 1 0 31 120 23 1.1 1 0 23 121 31 1.1 1 0 31 122 50 1.1 1 0 50 123 27 1.1 1 0 27 124 24 1.1 1 0 24 125 39 1.1 1 0 39 126 22 1.1 1 0 22 127 22 1.1 1 0 22 128 30 1.1 1 0 30 129 38 1.1 1 0 38 130 16 1.1 1 0 16 131 35 1.1 1 0 35 132 34 1.1 1 0 34 133 14 1.1 1 0 14 134 22 1.1 1 0 22 135 19 1.1 1 0 19 136 20 1.1 1 0 20 137 14 1.1 1 0 14 138 11 1.1 1 0 11 139 17 1.1 1 0 17 140 12 1.1 1 0 12 141 13 1.1 1 0 13 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz ============================================= 71733777 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 71733777 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1178612 (1.64%)