SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.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_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1.10 s (27 us/read; 2.25 M reads/minute). === Summary === Total reads processed: 41,244 Reads with adapters: 20,983 (50.9%) Reads written (passing filters): 41,244 (100.0%) Total basepairs processed: 5,533,654 bp Quality-trimmed: 11,962 bp (0.2%) Total written (filtered): 5,452,710 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20983 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.6% C: 21.7% G: 13.3% T: 26.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 15569 10311.0 0 15569 2 2875 2577.8 0 2875 3 1260 644.4 0 1260 4 347 161.1 0 347 5 17 40.3 0 17 6 20 10.1 0 20 7 14 2.5 0 14 8 9 0.6 0 9 9 9 0.2 0 8 1 10 22 0.0 1 15 7 11 19 0.0 1 13 6 12 26 0.0 1 15 11 14 23 0.0 1 12 11 15 25 0.0 1 16 9 17 14 0.0 1 11 3 18 17 0.0 1 14 3 19 23 0.0 1 16 7 20 14 0.0 1 10 4 21 10 0.0 1 6 4 22 19 0.0 1 13 6 23 16 0.0 1 10 6 24 28 0.0 1 20 8 25 13 0.0 1 9 4 26 10 0.0 1 8 2 27 10 0.0 1 5 5 28 15 0.0 1 13 2 29 6 0.0 1 4 2 30 22 0.0 1 18 4 31 11 0.0 1 8 3 32 18 0.0 1 13 5 33 20 0.0 1 17 3 34 10 0.0 1 6 4 35 14 0.0 1 7 7 36 10 0.0 1 8 2 37 9 0.0 1 8 1 38 6 0.0 1 2 4 39 7 0.0 1 5 2 41 11 0.0 1 10 1 42 15 0.0 1 11 4 43 7 0.0 1 5 2 44 11 0.0 1 7 4 45 18 0.0 1 14 4 46 9 0.0 1 6 3 47 7 0.0 1 4 3 48 23 0.0 1 20 3 49 8 0.0 1 5 3 50 1 0.0 1 1 51 13 0.0 1 11 2 52 8 0.0 1 7 1 53 11 0.0 1 6 5 54 10 0.0 1 8 2 55 2 0.0 1 2 56 1 0.0 1 0 1 57 5 0.0 1 3 2 58 4 0.0 1 4 59 3 0.0 1 2 1 60 4 0.0 1 3 1 62 4 0.0 1 3 1 63 4 0.0 1 4 64 5 0.0 1 4 1 65 2 0.0 1 0 2 66 9 0.0 1 4 5 67 6 0.0 1 4 2 68 6 0.0 1 5 1 69 5 0.0 1 3 2 70 6 0.0 1 5 1 71 5 0.0 1 4 1 72 6 0.0 1 3 3 73 7 0.0 1 5 2 74 8 0.0 1 6 2 75 1 0.0 1 0 1 76 5 0.0 1 4 1 77 4 0.0 1 2 2 78 7 0.0 1 7 79 5 0.0 1 4 1 80 5 0.0 1 3 2 81 7 0.0 1 5 2 82 4 0.0 1 4 83 6 0.0 1 5 1 84 3 0.0 1 2 1 85 3 0.0 1 3 86 6 0.0 1 4 2 87 4 0.0 1 3 1 88 5 0.0 1 3 2 89 9 0.0 1 4 5 90 5 0.0 1 4 1 91 4 0.0 1 3 1 92 2 0.0 1 1 1 93 2 0.0 1 1 1 94 2 0.0 1 0 2 95 3 0.0 1 1 2 96 8 0.0 1 5 3 97 2 0.0 1 2 98 7 0.0 1 6 1 99 1 0.0 1 1 100 2 0.0 1 1 1 101 2 0.0 1 1 1 102 2 0.0 1 2 103 4 0.0 1 3 1 104 1 0.0 1 1 105 1 0.0 1 1 106 3 0.0 1 2 1 107 2 0.0 1 0 2 109 3 0.0 1 3 111 1 0.0 1 1 112 1 0.0 1 1 113 1 0.0 1 0 1 115 3 0.0 1 1 2 118 1 0.0 1 0 1 119 3 0.0 1 1 2 120 1 0.0 1 1 121 1 0.0 1 0 1 122 1 0.0 1 1 124 1 0.0 1 1 126 2 0.0 1 1 1 127 3 0.0 1 2 1 128 1 0.0 1 1 130 1 0.0 1 0 1 131 3 0.0 1 2 1 135 1 0.0 1 1 137 1 0.0 1 0 1 138 1 0.0 1 0 1 139 1 0.0 1 1 140 1 0.0 1 1 150 2 0.0 1 1 1 151 21 0.0 1 11 10 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz ============================================= 41244 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 41244 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 208 (0.50%)