SUMMARISING RUN PARAMETERS ========================== Input filename: SRR13207060_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: 24). 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 SRR13207060_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 772.844 s (16.144 µs/read; 3.72 M reads/minute). === Summary === Total reads processed: 47,871,006 Reads with adapters: 20,525,648 (42.9%) Reads written (passing filters): 47,871,006 (100.0%) Total basepairs processed: 6,042,854,501 bp Quality-trimmed: 1,702,355 bp (0.0%) Total written (filtered): 6,017,085,418 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20525648 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 9.9% G: 5.8% T: 38.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 18406616 11967751.5 0 18406616 2 1361487 2991937.9 0 1361487 3 391002 747984.5 0 391002 4 266858 186996.1 0 266858 5 55111 46749.0 0 55111 6 13358 11687.3 0 13358 7 9112 2921.8 0 9112 8 6597 730.5 0 6597 9 2003 182.6 0 1676 327 10 12450 45.7 1 11470 980 11 128 11.4 1 23 105 12 41 2.9 1 10 31 13 12 0.7 1 3 9 14 6 0.7 1 1 5 15 6 0.7 1 3 3 16 1 0.7 1 1 17 6 0.7 1 3 3 18 2 0.7 1 0 2 19 9 0.7 1 6 3 20 5 0.7 1 3 2 21 4 0.7 1 3 1 22 7 0.7 1 6 1 23 1 0.7 1 0 1 24 9 0.7 1 4 5 25 4 0.7 1 3 1 26 3 0.7 1 3 27 4 0.7 1 0 4 28 4 0.7 1 2 2 29 2 0.7 1 2 30 6 0.7 1 5 1 31 1 0.7 1 0 1 32 9 0.7 1 6 3 33 3 0.7 1 2 1 34 3 0.7 1 3 35 6 0.7 1 2 4 36 5 0.7 1 2 3 37 7 0.7 1 5 2 38 4 0.7 1 2 2 39 5 0.7 1 3 2 40 5 0.7 1 4 1 41 2 0.7 1 1 1 42 5 0.7 1 3 2 43 4 0.7 1 3 1 44 5 0.7 1 4 1 45 6 0.7 1 5 1 46 1 0.7 1 1 47 7 0.7 1 5 2 48 6 0.7 1 4 2 49 5 0.7 1 4 1 50 4 0.7 1 3 1 51 2 0.7 1 2 52 4 0.7 1 3 1 53 7 0.7 1 4 3 54 6 0.7 1 4 2 55 7 0.7 1 6 1 56 5 0.7 1 4 1 57 6 0.7 1 2 4 58 5 0.7 1 3 2 59 1 0.7 1 0 1 60 12 0.7 1 8 4 61 2 0.7 1 2 62 2 0.7 1 2 63 6 0.7 1 5 1 64 1 0.7 1 1 65 3 0.7 1 1 2 66 13 0.7 1 12 1 67 3 0.7 1 3 68 5 0.7 1 2 3 69 3 0.7 1 2 1 70 3 0.7 1 3 71 1 0.7 1 0 1 72 3 0.7 1 3 73 1 0.7 1 1 74 4 0.7 1 3 1 75 6 0.7 1 4 2 76 7 0.7 1 5 2 77 7 0.7 1 2 5 78 4 0.7 1 4 79 4 0.7 1 4 80 7 0.7 1 5 2 81 1 0.7 1 0 1 82 3 0.7 1 2 1 83 4 0.7 1 2 2 84 6 0.7 1 4 2 85 8 0.7 1 8 86 6 0.7 1 6 87 2 0.7 1 2 88 3 0.7 1 3 89 3 0.7 1 3 90 4 0.7 1 2 2 91 4 0.7 1 3 1 92 5 0.7 1 3 2 93 6 0.7 1 4 2 94 3 0.7 1 3 95 3 0.7 1 3 96 13 0.7 1 10 3 97 13 0.7 1 11 2 98 4 0.7 1 3 1 99 6 0.7 1 4 2 100 7 0.7 1 4 3 101 6 0.7 1 6 102 7 0.7 1 6 1 103 5 0.7 1 2 3 104 9 0.7 1 7 2 105 7 0.7 1 5 2 106 8 0.7 1 8 107 8 0.7 1 7 1 108 7 0.7 1 6 1 109 9 0.7 1 9 110 9 0.7 1 9 111 4 0.7 1 3 1 112 5 0.7 1 5 113 13 0.7 1 11 2 114 7 0.7 1 7 115 16 0.7 1 16 116 16 0.7 1 15 1 117 25 0.7 1 22 3 118 11 0.7 1 10 1 119 24 0.7 1 22 2 120 9 0.7 1 8 1 121 14 0.7 1 13 1 122 9 0.7 1 7 2 123 13 0.7 1 11 2 124 11 0.7 1 8 3 125 13 0.7 1 10 3 126 10 0.7 1 9 1 127 14 0.7 1 14 128 10 0.7 1 9 1 129 25 0.7 1 22 3 130 13 0.7 1 10 3 131 15 0.7 1 14 1 132 33 0.7 1 26 7 133 24 0.7 1 22 2 134 18 0.7 1 10 8 135 30 0.7 1 13 17 RUN STATISTICS FOR INPUT FILE: SRR13207060_2.fastq.gz ============================================= 47871006 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 47871006 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3423 (0.01%)