SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_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_3_S1_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 2440.19 s (28 us/read; 2.16 M reads/minute). === Summary === Total reads processed: 87,950,295 Reads with adapters: 43,354,347 (49.3%) Reads written (passing filters): 87,950,295 (100.0%) Total basepairs processed: 9,821,337,199 bp Quality-trimmed: 7,779,520 bp (0.1%) Total written (filtered): 9,755,934,901 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43354347 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.0% C: 21.4% G: 14.8% T: 25.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32474107 21987573.8 0 32474107 2 8337730 5496893.4 0 8337730 3 2230881 1374223.4 0 2230881 4 175628 343555.8 0 175628 5 104322 85889.0 0 104322 6 13872 21472.2 0 13872 7 2929 5368.1 0 2929 8 554 1342.0 0 554 9 2956 335.5 0 202 2754 10 4757 83.9 1 98 4659 11 1287 21.0 1 6 1281 12 222 5.2 1 0 222 13 69 1.3 1 0 69 14 47 1.3 1 0 47 15 62 1.3 1 0 62 16 38 1.3 1 0 38 17 54 1.3 1 0 54 18 60 1.3 1 0 60 19 58 1.3 1 1 57 20 63 1.3 1 0 63 21 45 1.3 1 0 45 22 59 1.3 1 0 59 23 48 1.3 1 0 48 24 53 1.3 1 0 53 25 65 1.3 1 0 65 26 38 1.3 1 0 38 27 28 1.3 1 0 28 28 43 1.3 1 1 42 29 67 1.3 1 0 67 30 42 1.3 1 0 42 31 42 1.3 1 0 42 32 31 1.3 1 0 31 33 46 1.3 1 0 46 34 57 1.3 1 0 57 35 47 1.3 1 0 47 36 60 1.3 1 0 60 37 49 1.3 1 0 49 38 47 1.3 1 0 47 39 40 1.3 1 0 40 40 59 1.3 1 0 59 41 48 1.3 1 0 48 42 38 1.3 1 0 38 43 46 1.3 1 0 46 44 39 1.3 1 0 39 45 77 1.3 1 0 77 46 40 1.3 1 0 40 47 37 1.3 1 0 37 48 59 1.3 1 0 59 49 54 1.3 1 0 54 50 49 1.3 1 1 48 51 49 1.3 1 0 49 52 41 1.3 1 0 41 53 35 1.3 1 0 35 54 40 1.3 1 0 40 55 39 1.3 1 0 39 56 28 1.3 1 1 27 57 42 1.3 1 0 42 58 49 1.3 1 0 49 59 45 1.3 1 0 45 60 28 1.3 1 0 28 61 36 1.3 1 0 36 62 49 1.3 1 0 49 63 32 1.3 1 0 32 64 47 1.3 1 1 46 65 32 1.3 1 1 31 66 49 1.3 1 0 49 67 43 1.3 1 0 43 68 33 1.3 1 0 33 69 38 1.3 1 0 38 70 38 1.3 1 1 37 71 44 1.3 1 0 44 72 44 1.3 1 0 44 73 31 1.3 1 0 31 74 37 1.3 1 0 37 75 33 1.3 1 1 32 76 43 1.3 1 0 43 77 50 1.3 1 0 50 78 24 1.3 1 0 24 79 23 1.3 1 0 23 80 27 1.3 1 0 27 81 30 1.3 1 0 30 82 35 1.3 1 1 34 83 50 1.3 1 1 49 84 34 1.3 1 0 34 85 37 1.3 1 0 37 86 46 1.3 1 0 46 87 43 1.3 1 0 43 88 23 1.3 1 0 23 89 41 1.3 1 0 41 90 35 1.3 1 0 35 91 45 1.3 1 0 45 92 29 1.3 1 0 29 93 41 1.3 1 0 41 94 24 1.3 1 0 24 95 38 1.3 1 0 38 96 36 1.3 1 0 36 97 41 1.3 1 0 41 98 35 1.3 1 0 35 99 34 1.3 1 0 34 100 37 1.3 1 0 37 101 28 1.3 1 0 28 102 24 1.3 1 0 24 103 47 1.3 1 0 47 104 32 1.3 1 2 30 105 48 1.3 1 0 48 106 39 1.3 1 0 39 107 35 1.3 1 0 35 108 24 1.3 1 0 24 109 31 1.3 1 0 31 110 31 1.3 1 0 31 111 39 1.3 1 0 39 112 42 1.3 1 0 42 113 52 1.3 1 0 52 114 33 1.3 1 0 33 115 35 1.3 1 0 35 116 47 1.3 1 0 47 117 34 1.3 1 0 34 118 44 1.3 1 0 44 119 22 1.3 1 0 22 120 24 1.3 1 0 24 121 22 1.3 1 0 22 122 24 1.3 1 0 24 123 43 1.3 1 0 43 124 33 1.3 1 0 33 125 31 1.3 1 0 31 126 42 1.3 1 0 42 127 31 1.3 1 0 31 128 20 1.3 1 0 20 129 33 1.3 1 0 33 130 26 1.3 1 0 26 131 28 1.3 1 0 28 132 54 1.3 1 0 54 133 31 1.3 1 0 31 134 34 1.3 1 0 34 135 29 1.3 1 0 29 136 24 1.3 1 0 24 137 45 1.3 1 0 45 138 26 1.3 1 0 26 139 18 1.3 1 0 18 140 6 1.3 1 0 6 141 4 1.3 1 0 4 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz ============================================= 87950295 sequences processed in total