SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_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_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 0.61 s (27 us/read; 2.18 M reads/minute). === Summary === Total reads processed: 22,310 Reads with adapters: 11,102 (49.8%) Reads written (passing filters): 22,310 (100.0%) Total basepairs processed: 2,948,137 bp Quality-trimmed: 5,764 bp (0.2%) Total written (filtered): 2,883,202 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11102 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.2% C: 22.4% G: 13.8% T: 26.4% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 7858 5577.5 0 7858 2 1557 1394.4 0 1557 3 609 348.6 0 609 4 171 87.1 0 171 5 12 21.8 0 12 6 17 5.4 0 17 7 12 1.4 0 12 8 12 0.3 0 12 9 5 0.1 0 5 10 18 0.0 1 15 3 11 10 0.0 1 9 1 12 22 0.0 1 15 7 14 17 0.0 1 13 4 15 21 0.0 1 19 2 17 26 0.0 1 19 7 18 15 0.0 1 13 2 19 21 0.0 1 16 5 20 15 0.0 1 13 2 21 11 0.0 1 9 2 22 10 0.0 1 5 5 23 18 0.0 1 14 4 24 15 0.0 1 8 7 25 13 0.0 1 11 2 26 12 0.0 1 9 3 27 10 0.0 1 6 4 28 21 0.0 1 18 3 29 12 0.0 1 8 4 30 17 0.0 1 15 2 31 8 0.0 1 6 2 32 20 0.0 1 18 2 33 13 0.0 1 9 4 34 3 0.0 1 3 35 21 0.0 1 17 4 36 13 0.0 1 10 3 37 13 0.0 1 9 4 38 2 0.0 1 2 39 8 0.0 1 3 5 40 1 0.0 1 0 1 41 6 0.0 1 5 1 42 8 0.0 1 6 2 43 4 0.0 1 4 44 9 0.0 1 7 2 45 21 0.0 1 18 3 46 9 0.0 1 6 3 47 5 0.0 1 3 2 48 18 0.0 1 15 3 49 3 0.0 1 3 50 2 0.0 1 1 1 51 10 0.0 1 10 52 25 0.0 1 20 5 53 10 0.0 1 8 2 54 7 0.0 1 5 2 55 4 0.0 1 3 1 56 4 0.0 1 4 57 5 0.0 1 2 3 58 9 0.0 1 6 3 59 1 0.0 1 1 60 4 0.0 1 3 1 61 3 0.0 1 3 62 1 0.0 1 1 63 3 0.0 1 3 64 3 0.0 1 2 1 65 3 0.0 1 2 1 66 8 0.0 1 6 2 67 3 0.0 1 3 68 7 0.0 1 7 69 11 0.0 1 7 4 70 3 0.0 1 3 71 4 0.0 1 3 1 72 5 0.0 1 3 2 73 4 0.0 1 4 74 7 0.0 1 6 1 75 2 0.0 1 2 76 3 0.0 1 3 77 4 0.0 1 2 2 78 6 0.0 1 6 79 5 0.0 1 4 1 80 6 0.0 1 4 2 81 6 0.0 1 4 2 82 3 0.0 1 3 83 6 0.0 1 4 2 84 2 0.0 1 1 1 85 6 0.0 1 6 86 5 0.0 1 2 3 87 2 0.0 1 1 1 88 1 0.0 1 0 1 89 10 0.0 1 4 6 90 5 0.0 1 4 1 91 6 0.0 1 3 3 92 2 0.0 1 1 1 93 1 0.0 1 1 94 3 0.0 1 1 2 95 9 0.0 1 7 2 96 3 0.0 1 3 97 3 0.0 1 2 1 98 3 0.0 1 3 99 5 0.0 1 5 100 4 0.0 1 1 3 101 4 0.0 1 3 1 102 2 0.0 1 2 103 2 0.0 1 2 104 1 0.0 1 0 1 107 4 0.0 1 3 1 108 3 0.0 1 3 109 1 0.0 1 1 110 5 0.0 1 4 1 111 1 0.0 1 1 116 2 0.0 1 1 1 117 2 0.0 1 2 118 3 0.0 1 2 1 119 3 0.0 1 3 120 2 0.0 1 0 2 121 5 0.0 1 5 123 2 0.0 1 2 124 1 0.0 1 1 126 3 0.0 1 3 127 2 0.0 1 1 1 129 1 0.0 1 1 131 4 0.0 1 3 1 132 2 0.0 1 2 133 2 0.0 1 2 134 1 0.0 1 0 1 135 5 0.0 1 4 1 137 4 0.0 1 4 139 1 0.0 1 1 143 1 0.0 1 0 1 144 1 0.0 1 0 1 146 1 0.0 1 1 148 1 0.0 1 0 1 151 31 0.0 1 22 9 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz ============================================= 22310 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22310 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 159 (0.71%)