SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_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_1_S3_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 2647.70 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 82,999,052 Reads with adapters: 41,700,384 (50.2%) Reads written (passing filters): 82,999,052 (100.0%) Total basepairs processed: 10,399,588,050 bp Quality-trimmed: 7,072,599 bp (0.1%) Total written (filtered): 10,336,922,292 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 41700384 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.4% C: 21.5% G: 15.5% T: 24.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 31152549 20749763.0 0 31152549 2 8123960 5187440.8 0 8123960 3 2136355 1296860.2 0 2136355 4 178787 324215.0 0 178787 5 72465 81053.8 0 72465 6 17460 20263.4 0 17460 7 3839 5065.9 0 3839 8 543 1266.5 0 543 9 2556 316.6 0 214 2342 10 3325 79.2 1 82 3243 11 1240 19.8 1 14 1226 12 328 4.9 1 5 323 13 96 1.2 1 0 96 14 52 1.2 1 3 49 15 87 1.2 1 2 85 16 62 1.2 1 1 61 17 92 1.2 1 0 92 18 53 1.2 1 0 53 19 63 1.2 1 1 62 20 72 1.2 1 0 72 21 72 1.2 1 0 72 22 74 1.2 1 0 74 23 52 1.2 1 0 52 24 73 1.2 1 0 73 25 73 1.2 1 0 73 26 36 1.2 1 0 36 27 63 1.2 1 0 63 28 60 1.2 1 2 58 29 86 1.2 1 0 86 30 68 1.2 1 1 67 31 92 1.2 1 0 92 32 48 1.2 1 0 48 33 71 1.2 1 0 71 34 61 1.2 1 0 61 35 74 1.2 1 0 74 36 55 1.2 1 0 55 37 57 1.2 1 0 57 38 51 1.2 1 0 51 39 58 1.2 1 0 58 40 71 1.2 1 4 67 41 55 1.2 1 1 54 42 49 1.2 1 1 48 43 66 1.2 1 2 64 44 46 1.2 1 1 45 45 73 1.2 1 0 73 46 59 1.2 1 1 58 47 44 1.2 1 0 44 48 69 1.2 1 0 69 49 54 1.2 1 1 53 50 70 1.2 1 1 69 51 56 1.2 1 0 56 52 54 1.2 1 1 53 53 37 1.2 1 0 37 54 52 1.2 1 0 52 55 53 1.2 1 1 52 56 55 1.2 1 0 55 57 63 1.2 1 2 61 58 62 1.2 1 0 62 59 43 1.2 1 0 43 60 66 1.2 1 0 66 61 56 1.2 1 0 56 62 76 1.2 1 0 76 63 47 1.2 1 0 47 64 59 1.2 1 0 59 65 85 1.2 1 0 85 66 47 1.2 1 0 47 67 45 1.2 1 0 45 68 44 1.2 1 0 44 69 58 1.2 1 0 58 70 66 1.2 1 0 66 71 46 1.2 1 0 46 72 50 1.2 1 1 49 73 47 1.2 1 0 47 74 33 1.2 1 0 33 75 51 1.2 1 0 51 76 27 1.2 1 0 27 77 44 1.2 1 0 44 78 55 1.2 1 0 55 79 68 1.2 1 0 68 80 45 1.2 1 1 44 81 39 1.2 1 0 39 82 69 1.2 1 0 69 83 47 1.2 1 1 46 84 72 1.2 1 0 72 85 78 1.2 1 0 78 86 57 1.2 1 0 57 87 62 1.2 1 0 62 88 53 1.2 1 0 53 89 45 1.2 1 0 45 90 52 1.2 1 0 52 91 74 1.2 1 0 74 92 55 1.2 1 0 55 93 52 1.2 1 0 52 94 51 1.2 1 0 51 95 43 1.2 1 0 43 96 71 1.2 1 0 71 97 58 1.2 1 0 58 98 31 1.2 1 0 31 99 60 1.2 1 0 60 100 51 1.2 1 0 51 101 47 1.2 1 0 47 102 36 1.2 1 0 36 103 51 1.2 1 0 51 104 62 1.2 1 0 62 105 53 1.2 1 0 53 106 34 1.2 1 0 34 107 65 1.2 1 1 64 108 55 1.2 1 0 55 109 39 1.2 1 0 39 110 40 1.2 1 0 40 111 50 1.2 1 0 50 112 48 1.2 1 0 48 113 38 1.2 1 0 38 114 55 1.2 1 0 55 115 47 1.2 1 0 47 116 68 1.2 1 1 67 117 53 1.2 1 0 53 118 41 1.2 1 0 41 119 49 1.2 1 0 49 120 31 1.2 1 0 31 121 47 1.2 1 0 47 122 45 1.2 1 0 45 123 52 1.2 1 0 52 124 24 1.2 1 0 24 125 49 1.2 1 0 49 126 43 1.2 1 0 43 127 46 1.2 1 0 46 128 59 1.2 1 0 59 129 41 1.2 1 0 41 130 47 1.2 1 0 47 131 50 1.2 1 0 50 132 48 1.2 1 0 48 133 58 1.2 1 0 58 134 40 1.2 1 0 40 135 46 1.2 1 0 46 136 35 1.2 1 0 35 137 34 1.2 1 0 34 138 38 1.2 1 0 38 139 15 1.2 1 0 15 140 21 1.2 1 0 21 141 10 1.2 1 0 10 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz ============================================= 82999052 sequences processed in total