SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041623_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.2 Cutadapt version: 2.6 Number of cores used for trimming: 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases Output file will be GZIP compressed This is cutadapt 2.6 with Python 3.6.7 Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC /sibcb2/bioinformatics2/heshutao/processing/cup/BS_workflow/20201104_20201106/tmp/5f253770-48bc-11eb-adb9-b4055d0383c6/trimmed/RRBS20A041623_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 2.64 s (23 us/read; 2.59 M reads/minute). === Summary === Total reads processed: 113,686 Reads with adapters: 46,218 (40.7%) Reads written (passing filters): 113,686 (100.0%) Total basepairs processed: 10,512,420 bp Total written (filtered): 10,370,414 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46218 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.7% C: 2.4% G: 19.7% T: 44.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33294 28421.5 0 33294 2 8960 7105.4 0 8960 3 2094 1776.3 0 2094 4 544 444.1 0 544 5 28 111.0 0 28 6 8 27.8 0 8 7 10 6.9 0 10 8 6 1.7 0 6 9 2 0.4 0 2 10 8 0.1 1 4 4 11 18 0.0 1 0 18 12 10 0.0 1 0 10 13 2 0.0 1 2 14 8 0.0 1 2 6 15 10 0.0 1 2 8 16 22 0.0 1 2 20 17 24 0.0 1 4 20 18 18 0.0 1 0 18 20 8 0.0 1 2 6 23 12 0.0 1 4 8 24 16 0.0 1 6 10 25 16 0.0 1 2 14 26 4 0.0 1 0 4 27 8 0.0 1 0 8 28 26 0.0 1 6 20 29 20 0.0 1 2 18 30 12 0.0 1 0 12 32 12 0.0 1 0 12 33 18 0.0 1 2 16 34 26 0.0 1 6 20 35 22 0.0 1 0 22 36 8 0.0 1 0 8 37 26 0.0 1 8 18 38 6 0.0 1 2 4 39 2 0.0 1 0 2 40 6 0.0 1 0 6 41 16 0.0 1 2 14 42 18 0.0 1 2 16 43 22 0.0 1 0 22 44 10 0.0 1 0 10 45 12 0.0 1 2 10 46 6 0.0 1 0 6 47 10 0.0 1 2 8 48 20 0.0 1 4 16 50 16 0.0 1 4 12 51 12 0.0 1 0 12 52 8 0.0 1 0 8 53 20 0.0 1 0 20 54 26 0.0 1 2 24 55 14 0.0 1 2 12 56 18 0.0 1 6 12 57 16 0.0 1 2 14 58 14 0.0 1 0 14 59 10 0.0 1 2 8 60 6 0.0 1 2 4 61 26 0.0 1 4 22 62 66 0.0 1 4 62 63 16 0.0 1 4 12 64 2 0.0 1 2 65 4 0.0 1 0 4 66 10 0.0 1 0 10 67 2 0.0 1 0 2 68 20 0.0 1 8 12 69 18 0.0 1 2 16 70 32 0.0 1 0 32 71 6 0.0 1 0 6 72 6 0.0 1 0 6 73 2 0.0 1 0 2 76 2 0.0 1 2 77 4 0.0 1 0 4 78 6 0.0 1 2 4 79 6 0.0 1 0 6 80 6 0.0 1 2 4 81 16 0.0 1 2 14 82 6 0.0 1 2 4 83 12 0.0 1 0 12 84 8 0.0 1 2 6 85 18 0.0 1 4 14 86 4 0.0 1 2 2 87 10 0.0 1 0 10 88 8 0.0 1 4 4 89 8 0.0 1 2 6 90 12 0.0 1 0 12 91 8 0.0 1 2 6 92 14 0.0 1 2 12 93 26 0.0 1 4 22 94 40 0.0 1 6 34 95 8 0.0 1 0 8 97 18 0.0 1 2 16 98 6 0.0 1 2 4 99 4 0.0 1 0 4 100 2 0.0 1 0 2 101 2 0.0 1 0 2 102 4 0.0 1 0 4 103 2 0.0 1 2 105 2 0.0 1 0 2 106 2 0.0 1 2 107 2 0.0 1 0 2 110 2 0.0 1 0 2 137 8 0.0 1 8 138 144 0.0 1 138 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041623_val_1.fq.gz ============================================= 113686 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7344 (6.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 46218 (40.7%)