SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1.13 s (27 us/read; 2.19 M reads/minute). === Summary === Total reads processed: 41,244 Reads with adapters: 22,174 (53.8%) Reads written (passing filters): 41,244 (100.0%) Total basepairs processed: 5,571,801 bp Quality-trimmed: 10,796 bp (0.2%) Total written (filtered): 5,496,658 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22174 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.0% C: 22.0% G: 10.3% T: 26.5% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 17489 10311.0 0 17489 2 2472 2577.8 0 2472 3 1088 644.4 0 1088 4 354 161.1 0 354 5 17 40.3 0 17 6 10 10.1 0 10 7 9 2.5 0 9 8 9 0.6 0 9 9 9 0.2 0 9 10 16 0.0 1 11 5 11 16 0.0 1 12 4 12 18 0.0 1 16 2 13 2 0.0 1 2 14 23 0.0 1 15 8 15 1 0.0 1 1 16 25 0.0 1 11 14 17 1 0.0 1 1 18 29 0.0 1 20 9 19 29 0.0 1 19 10 21 1 0.0 1 1 22 1 0.0 1 0 1 23 15 0.0 1 11 4 24 32 0.0 1 20 12 25 1 0.0 1 1 26 7 0.0 1 6 1 27 10 0.0 1 9 1 29 9 0.0 1 6 3 30 13 0.0 1 11 2 31 15 0.0 1 10 5 32 2 0.0 1 1 1 33 24 0.0 1 21 3 35 18 0.0 1 13 5 36 11 0.0 1 9 2 37 5 0.0 1 3 2 38 8 0.0 1 5 3 39 11 0.0 1 8 3 40 12 0.0 1 11 1 41 1 0.0 1 0 1 42 12 0.0 1 8 4 43 20 0.0 1 10 10 44 27 0.0 1 20 7 45 6 0.0 1 5 1 46 8 0.0 1 5 3 48 32 0.0 1 18 14 49 14 0.0 1 10 4 50 6 0.0 1 4 2 51 9 0.0 1 8 1 52 10 0.0 1 8 2 53 3 0.0 1 2 1 55 2 0.0 1 2 56 9 0.0 1 7 2 58 3 0.0 1 3 59 6 0.0 1 3 3 61 1 0.0 1 1 62 3 0.0 1 3 63 1 0.0 1 1 64 1 0.0 1 1 65 1 0.0 1 0 1 66 3 0.0 1 2 1 67 4 0.0 1 3 1 68 2 0.0 1 1 1 69 2 0.0 1 1 1 70 3 0.0 1 3 71 2 0.0 1 0 2 72 1 0.0 1 0 1 73 4 0.0 1 4 74 5 0.0 1 3 2 75 1 0.0 1 0 1 76 1 0.0 1 0 1 77 2 0.0 1 2 78 3 0.0 1 2 1 79 4 0.0 1 2 2 80 3 0.0 1 3 81 4 0.0 1 3 1 82 7 0.0 1 7 83 6 0.0 1 5 1 84 3 0.0 1 2 1 85 4 0.0 1 3 1 86 6 0.0 1 5 1 87 2 0.0 1 1 1 88 1 0.0 1 1 89 3 0.0 1 2 1 90 7 0.0 1 5 2 91 4 0.0 1 3 1 93 3 0.0 1 2 1 94 1 0.0 1 1 95 3 0.0 1 2 1 96 3 0.0 1 2 1 97 1 0.0 1 1 98 4 0.0 1 4 100 2 0.0 1 1 1 101 1 0.0 1 0 1 102 1 0.0 1 1 104 3 0.0 1 1 2 105 1 0.0 1 1 106 2 0.0 1 1 1 107 2 0.0 1 0 2 109 2 0.0 1 2 111 3 0.0 1 2 1 115 1 0.0 1 1 116 2 0.0 1 2 119 2 0.0 1 1 1 120 1 0.0 1 1 121 2 0.0 1 0 2 126 3 0.0 1 2 1 127 1 0.0 1 0 1 128 1 0.0 1 0 1 130 1 0.0 1 0 1 131 1 0.0 1 1 135 1 0.0 1 1 139 1 0.0 1 1 140 1 0.0 1 1 143 1 0.0 1 0 1 144 1 0.0 1 1 150 3 0.0 1 3 151 45 0.0 1 16 29 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz ============================================= 41244 sequences processed in total