SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041603_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/raw_data/cup/BS_workflow/20201028_merged/tmp/ab4f1cf4-3dd8-11eb-a99a-6c92bfc12eba/trimmed/RRBS20A041603_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1.93 s (23 us/read; 2.65 M reads/minute). === Summary === Total reads processed: 85,382 Reads with adapters: 37,484 (43.9%) Reads written (passing filters): 85,382 (100.0%) Total basepairs processed: 8,747,055 bp Total written (filtered): 8,638,769 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 37484 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.3% C: 0.9% G: 22.3% T: 46.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27428 21345.5 0 27428 2 7138 5336.4 0 7138 3 1645 1334.1 0 1645 4 396 333.5 0 396 5 14 83.4 0 14 6 9 20.8 0 9 7 9 5.2 0 9 8 6 1.3 0 6 9 25 0.3 0 23 2 10 11 0.1 1 1 10 11 16 0.0 1 3 13 12 8 0.0 1 1 7 13 3 0.0 1 0 3 14 9 0.0 1 1 8 15 10 0.0 1 4 6 16 32 0.0 1 5 27 17 22 0.0 1 1 21 18 14 0.0 1 3 11 19 1 0.0 1 0 1 20 6 0.0 1 0 6 21 1 0.0 1 0 1 23 6 0.0 1 1 5 24 10 0.0 1 2 8 25 7 0.0 1 2 5 26 2 0.0 1 0 2 27 9 0.0 1 1 8 28 9 0.0 1 3 6 29 15 0.0 1 1 14 30 3 0.0 1 1 2 31 2 0.0 1 0 2 32 4 0.0 1 0 4 33 12 0.0 1 2 10 34 10 0.0 1 1 9 35 10 0.0 1 2 8 36 7 0.0 1 1 6 37 13 0.0 1 2 11 38 3 0.0 1 0 3 39 1 0.0 1 0 1 40 15 0.0 1 2 13 41 5 0.0 1 0 5 42 11 0.0 1 2 9 43 25 0.0 1 6 19 44 4 0.0 1 0 4 45 11 0.0 1 2 9 46 4 0.0 1 2 2 47 6 0.0 1 0 6 48 18 0.0 1 4 14 49 2 0.0 1 0 2 50 7 0.0 1 1 6 53 4 0.0 1 0 4 54 18 0.0 1 1 17 55 15 0.0 1 3 12 56 4 0.0 1 1 3 57 6 0.0 1 1 5 58 2 0.0 1 0 2 59 2 0.0 1 0 2 60 5 0.0 1 2 3 61 10 0.0 1 1 9 62 18 0.0 1 4 14 63 5 0.0 1 2 3 65 1 0.0 1 0 1 66 3 0.0 1 0 3 68 3 0.0 1 0 3 69 7 0.0 1 0 7 70 8 0.0 1 0 8 71 2 0.0 1 1 1 72 2 0.0 1 1 1 73 3 0.0 1 2 1 74 2 0.0 1 0 2 75 3 0.0 1 1 2 76 8 0.0 1 1 7 77 2 0.0 1 0 2 79 2 0.0 1 1 1 80 1 0.0 1 0 1 82 2 0.0 1 0 2 83 5 0.0 1 1 4 84 2 0.0 1 0 2 85 6 0.0 1 1 5 86 2 0.0 1 0 2 87 3 0.0 1 0 3 88 1 0.0 1 0 1 89 3 0.0 1 0 3 91 4 0.0 1 0 4 93 5 0.0 1 0 5 94 14 0.0 1 1 13 95 1 0.0 1 0 1 96 1 0.0 1 0 1 97 7 0.0 1 0 7 100 1 0.0 1 0 1 101 2 0.0 1 0 2 103 1 0.0 1 0 1 136 1 0.0 1 1 137 23 0.0 1 22 1 138 230 0.0 1 222 8 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041603_val_1.fq.gz ============================================= 85382 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4248 (5.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 37484 (43.9%)