SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_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_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.61 s (27 us/read; 2.20 M reads/minute). === Summary === Total reads processed: 22,310 Reads with adapters: 11,594 (52.0%) Reads written (passing filters): 22,310 (100.0%) Total basepairs processed: 3,005,909 bp Quality-trimmed: 4,316 bp (0.1%) Total written (filtered): 2,944,393 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11594 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.7% C: 22.0% G: 11.3% T: 26.4% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 8570 5577.5 0 8570 2 1444 1394.4 0 1444 3 596 348.6 0 596 4 178 87.1 0 178 5 11 21.8 0 11 6 13 5.4 0 13 7 8 1.4 0 8 8 9 0.3 0 9 9 8 0.1 0 7 1 10 23 0.0 1 18 5 11 15 0.0 1 7 8 12 24 0.0 1 18 6 13 2 0.0 1 1 1 14 19 0.0 1 16 3 16 23 0.0 1 16 7 17 1 0.0 1 1 18 22 0.0 1 19 3 19 34 0.0 1 30 4 22 1 0.0 1 1 23 14 0.0 1 10 4 24 24 0.0 1 18 6 25 2 0.0 1 1 1 26 7 0.0 1 5 2 27 10 0.0 1 8 2 29 16 0.0 1 14 2 30 12 0.0 1 10 2 31 12 0.0 1 7 5 32 3 0.0 1 0 3 33 25 0.0 1 24 1 34 1 0.0 1 1 35 20 0.0 1 12 8 36 12 0.0 1 9 3 37 14 0.0 1 9 5 38 6 0.0 1 4 2 39 3 0.0 1 2 1 40 15 0.0 1 8 7 41 2 0.0 1 1 1 42 12 0.0 1 8 4 43 13 0.0 1 11 2 44 16 0.0 1 13 3 45 3 0.0 1 3 46 6 0.0 1 4 2 47 1 0.0 1 0 1 48 19 0.0 1 16 3 49 8 0.0 1 8 50 2 0.0 1 2 51 8 0.0 1 6 2 52 11 0.0 1 9 2 53 2 0.0 1 1 1 54 3 0.0 1 3 55 13 0.0 1 11 2 56 7 0.0 1 5 2 57 3 0.0 1 2 1 58 2 0.0 1 1 1 59 11 0.0 1 9 2 61 7 0.0 1 3 4 62 6 0.0 1 5 1 63 3 0.0 1 2 1 64 1 0.0 1 1 65 4 0.0 1 1 3 66 6 0.0 1 3 3 67 2 0.0 1 2 68 3 0.0 1 2 1 69 4 0.0 1 3 1 70 6 0.0 1 4 2 71 1 0.0 1 0 1 72 1 0.0 1 1 73 5 0.0 1 4 1 74 2 0.0 1 2 75 3 0.0 1 3 76 2 0.0 1 1 1 77 4 0.0 1 3 1 78 4 0.0 1 4 79 4 0.0 1 4 80 4 0.0 1 3 1 81 8 0.0 1 8 82 1 0.0 1 1 83 4 0.0 1 4 84 1 0.0 1 1 85 4 0.0 1 4 86 5 0.0 1 4 1 87 1 0.0 1 0 1 89 4 0.0 1 4 90 4 0.0 1 4 91 4 0.0 1 4 93 2 0.0 1 1 1 94 2 0.0 1 2 95 7 0.0 1 5 2 96 2 0.0 1 1 1 97 4 0.0 1 4 98 2 0.0 1 2 99 2 0.0 1 1 1 100 1 0.0 1 0 1 101 5 0.0 1 4 1 102 3 0.0 1 2 1 103 2 0.0 1 2 107 1 0.0 1 1 108 1 0.0 1 1 109 1 0.0 1 1 110 4 0.0 1 3 1 111 2 0.0 1 1 1 112 1 0.0 1 1 116 2 0.0 1 2 117 1 0.0 1 1 118 2 0.0 1 2 119 3 0.0 1 3 120 2 0.0 1 1 1 121 2 0.0 1 2 123 1 0.0 1 1 124 1 0.0 1 1 126 1 0.0 1 1 127 2 0.0 1 1 1 129 2 0.0 1 1 1 131 4 0.0 1 3 1 132 1 0.0 1 1 133 3 0.0 1 2 1 135 3 0.0 1 3 136 1 0.0 1 0 1 137 3 0.0 1 3 138 1 0.0 1 1 139 1 0.0 1 1 143 1 0.0 1 1 146 1 0.0 1 1 149 1 0.0 1 0 1 150 2 0.0 1 2 151 64 0.0 1 36 28 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz ============================================= 22310 sequences processed in total