SUMMARISING RUN PARAMETERS ========================== Input filename: SRR13207066_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 20). Second best hit was smallRNA (count: 0) 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 4.2 with Python 3.10.8 Command line parameters: -j 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR13207066_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 677.739 s (16.634 µs/read; 3.61 M reads/minute). === Summary === Total reads processed: 40,743,756 Reads with adapters: 17,351,768 (42.6%) Reads written (passing filters): 40,743,756 (100.0%) Total basepairs processed: 5,120,592,948 bp Quality-trimmed: 1,710,015 bp (0.0%) Total written (filtered): 5,098,406,294 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17351768 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.2% G: 6.2% T: 38.1% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 15448638 10185939.0 0 15448638 2 1237821 2546484.8 0 1237821 3 352171 636621.2 0 352171 4 234395 159155.3 0 234395 5 42680 39788.8 0 42680 6 10437 9947.2 0 10437 7 7966 2486.8 0 7966 8 5733 621.7 0 5733 9 1586 155.4 0 1253 333 10 9480 38.9 1 8647 833 11 83 9.7 1 10 73 12 28 2.4 1 6 22 13 3 0.6 1 1 2 14 5 0.6 1 1 4 15 2 0.6 1 1 1 16 3 0.6 1 1 2 17 4 0.6 1 1 3 19 2 0.6 1 0 2 20 4 0.6 1 2 2 21 3 0.6 1 3 22 5 0.6 1 5 23 5 0.6 1 2 3 24 5 0.6 1 0 5 25 2 0.6 1 2 27 3 0.6 1 2 1 28 4 0.6 1 3 1 29 4 0.6 1 3 1 30 5 0.6 1 5 31 4 0.6 1 2 2 32 2 0.6 1 2 33 2 0.6 1 1 1 34 3 0.6 1 1 2 35 5 0.6 1 4 1 38 2 0.6 1 2 39 3 0.6 1 1 2 40 4 0.6 1 3 1 41 4 0.6 1 4 42 3 0.6 1 3 43 5 0.6 1 4 1 44 5 0.6 1 2 3 45 5 0.6 1 2 3 46 6 0.6 1 3 3 47 5 0.6 1 3 2 48 2 0.6 1 2 49 5 0.6 1 4 1 50 3 0.6 1 3 51 4 0.6 1 3 1 52 1 0.6 1 1 53 4 0.6 1 2 2 54 1 0.6 1 0 1 55 7 0.6 1 5 2 56 3 0.6 1 2 1 57 5 0.6 1 1 4 58 7 0.6 1 4 3 59 5 0.6 1 5 60 4 0.6 1 3 1 61 4 0.6 1 4 62 4 0.6 1 2 2 63 2 0.6 1 1 1 64 2 0.6 1 2 65 9 0.6 1 8 1 66 4 0.6 1 0 4 67 1 0.6 1 1 68 5 0.6 1 4 1 69 4 0.6 1 3 1 70 6 0.6 1 5 1 71 6 0.6 1 3 3 72 3 0.6 1 2 1 73 6 0.6 1 4 2 74 3 0.6 1 2 1 75 2 0.6 1 2 76 2 0.6 1 1 1 77 3 0.6 1 2 1 78 3 0.6 1 2 1 79 5 0.6 1 4 1 80 3 0.6 1 3 81 6 0.6 1 4 2 82 7 0.6 1 7 83 6 0.6 1 4 2 84 1 0.6 1 1 85 3 0.6 1 2 1 86 5 0.6 1 3 2 87 3 0.6 1 3 88 5 0.6 1 4 1 89 5 0.6 1 4 1 90 5 0.6 1 4 1 91 2 0.6 1 1 1 92 3 0.6 1 3 93 1 0.6 1 1 94 3 0.6 1 2 1 95 2 0.6 1 1 1 96 4 0.6 1 3 1 97 10 0.6 1 6 4 98 12 0.6 1 11 1 99 12 0.6 1 11 1 100 11 0.6 1 7 4 101 7 0.6 1 6 1 102 9 0.6 1 8 1 103 4 0.6 1 1 3 104 6 0.6 1 3 3 105 4 0.6 1 2 2 106 4 0.6 1 3 1 107 6 0.6 1 3 3 108 3 0.6 1 3 109 5 0.6 1 4 1 110 7 0.6 1 6 1 111 7 0.6 1 6 1 112 10 0.6 1 9 1 113 4 0.6 1 3 1 114 10 0.6 1 10 115 9 0.6 1 5 4 116 12 0.6 1 9 3 117 15 0.6 1 12 3 118 12 0.6 1 12 119 9 0.6 1 7 2 120 19 0.6 1 17 2 121 13 0.6 1 12 1 122 17 0.6 1 15 2 123 9 0.6 1 9 124 20 0.6 1 19 1 125 8 0.6 1 8 126 14 0.6 1 11 3 127 14 0.6 1 9 5 128 12 0.6 1 11 1 129 20 0.6 1 15 5 130 21 0.6 1 18 3 131 14 0.6 1 12 2 132 16 0.6 1 15 1 133 19 0.6 1 17 2 134 17 0.6 1 11 6 135 23 0.6 1 10 13 RUN STATISTICS FOR INPUT FILE: SRR13207066_2.fastq.gz ============================================= 40743756 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 40743756 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3689 (0.01%)