SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_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_1_S3_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 2757.68 s (33 us/read; 1.81 M reads/minute). === Summary === Total reads processed: 82,999,052 Reads with adapters: 29,185,201 (35.2%) Reads written (passing filters): 82,999,052 (100.0%) Total basepairs processed: 10,052,257,721 bp Quality-trimmed: 27,927,865 bp (0.3%) Total written (filtered): 9,990,844,321 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29185201 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.9% C: 22.1% G: 6.6% T: 24.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26290758 20749763.0 0 26290758 2 2135097 5187440.8 0 2135097 3 581764 1296860.2 0 581764 4 158432 324215.0 0 158432 5 5056 81053.8 0 5056 6 4203 20263.4 0 4203 7 1024 5065.9 0 1024 8 176 1266.5 0 176 9 798 316.6 0 196 602 10 852 79.2 1 12 840 11 345 19.8 1 1 344 12 109 4.9 1 0 109 13 59 1.2 1 0 59 14 56 1.2 1 0 56 15 48 1.2 1 0 48 16 51 1.2 1 0 51 17 63 1.2 1 0 63 18 63 1.2 1 1 62 19 71 1.2 1 0 71 20 56 1.2 1 0 56 21 52 1.2 1 2 50 22 54 1.2 1 1 53 23 84 1.2 1 2 82 24 53 1.2 1 2 51 25 74 1.2 1 0 74 26 84 1.2 1 0 84 27 51 1.2 1 0 51 28 78 1.2 1 0 78 29 54 1.2 1 0 54 30 53 1.2 1 0 53 31 47 1.2 1 0 47 32 50 1.2 1 1 49 33 55 1.2 1 0 55 34 70 1.2 1 1 69 35 45 1.2 1 0 45 36 42 1.2 1 0 42 37 65 1.2 1 0 65 38 61 1.2 1 0 61 39 54 1.2 1 0 54 40 76 1.2 1 0 76 41 61 1.2 1 0 61 42 45 1.2 1 0 45 43 44 1.2 1 0 44 44 67 1.2 1 0 67 45 67 1.2 1 0 67 46 73 1.2 1 1 72 47 59 1.2 1 1 58 48 64 1.2 1 0 64 49 40 1.2 1 0 40 50 58 1.2 1 0 58 51 63 1.2 1 0 63 52 44 1.2 1 1 43 53 57 1.2 1 0 57 54 34 1.2 1 0 34 55 55 1.2 1 0 55 56 72 1.2 1 0 72 57 51 1.2 1 0 51 58 52 1.2 1 0 52 59 46 1.2 1 0 46 60 51 1.2 1 0 51 61 62 1.2 1 3 59 62 64 1.2 1 0 64 63 66 1.2 1 0 66 64 44 1.2 1 2 42 65 51 1.2 1 0 51 66 65 1.2 1 0 65 67 62 1.2 1 0 62 68 66 1.2 1 0 66 69 60 1.2 1 0 60 70 68 1.2 1 0 68 71 53 1.2 1 0 53 72 69 1.2 1 0 69 73 54 1.2 1 0 54 74 52 1.2 1 0 52 75 67 1.2 1 0 67 76 39 1.2 1 0 39 77 54 1.2 1 0 54 78 61 1.2 1 0 61 79 42 1.2 1 0 42 80 45 1.2 1 0 45 81 49 1.2 1 0 49 82 67 1.2 1 0 67 83 85 1.2 1 0 85 84 55 1.2 1 0 55 85 45 1.2 1 0 45 86 44 1.2 1 0 44 87 49 1.2 1 0 49 88 60 1.2 1 0 60 89 67 1.2 1 0 67 90 53 1.2 1 0 53 91 47 1.2 1 0 47 92 44 1.2 1 0 44 93 45 1.2 1 0 45 94 56 1.2 1 0 56 95 53 1.2 1 1 52 96 69 1.2 1 0 69 97 43 1.2 1 0 43 98 40 1.2 1 0 40 99 67 1.2 1 0 67 100 44 1.2 1 0 44 101 44 1.2 1 0 44 102 45 1.2 1 0 45 103 60 1.2 1 0 60 104 63 1.2 1 0 63 105 35 1.2 1 0 35 106 51 1.2 1 0 51 107 46 1.2 1 0 46 108 32 1.2 1 0 32 109 47 1.2 1 0 47 110 34 1.2 1 0 34 111 44 1.2 1 0 44 112 36 1.2 1 0 36 113 54 1.2 1 0 54 114 36 1.2 1 0 36 115 50 1.2 1 0 50 116 49 1.2 1 0 49 117 46 1.2 1 0 46 118 55 1.2 1 0 55 119 32 1.2 1 0 32 120 41 1.2 1 0 41 121 34 1.2 1 0 34 122 58 1.2 1 0 58 123 36 1.2 1 0 36 124 47 1.2 1 0 47 125 35 1.2 1 0 35 126 33 1.2 1 0 33 127 32 1.2 1 0 32 128 46 1.2 1 0 46 129 42 1.2 1 0 42 130 43 1.2 1 0 43 131 57 1.2 1 0 57 132 32 1.2 1 0 32 133 33 1.2 1 0 33 134 40 1.2 1 0 40 135 23 1.2 1 0 23 136 23 1.2 1 0 23 137 19 1.2 1 0 19 138 9 1.2 1 0 9 139 19 1.2 1 0 19 140 26 1.2 1 0 26 141 2 1.2 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz ============================================= 82999052 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82999052 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1380605 (1.66%)