SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041603_val_2.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_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1.73 s (20 us/read; 2.96 M reads/minute). === Summary === Total reads processed: 85,382 Reads with adapters: 31,008 (36.3%) Reads written (passing filters): 85,382 (100.0%) Total basepairs processed: 8,597,111 bp Total written (filtered): 8,525,538 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31008 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.3% C: 78.4% G: 2.1% T: 5.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 30434 21345.5 0 30434 2 131 5336.4 0 131 3 10 1334.1 0 10 4 11 333.5 0 11 5 4 83.4 0 4 6 5 20.8 0 5 7 9 5.2 0 9 8 6 1.3 0 6 9 2 0.3 0 1 1 10 7 0.1 1 3 4 12 6 0.0 1 3 3 13 1 0.0 1 0 1 14 3 0.0 1 0 3 15 4 0.0 1 2 2 16 4 0.0 1 0 4 17 1 0.0 1 0 1 18 1 0.0 1 0 1 19 1 0.0 1 0 1 20 3 0.0 1 1 2 22 2 0.0 1 0 2 23 5 0.0 1 0 5 24 7 0.0 1 1 6 25 3 0.0 1 0 3 26 6 0.0 1 0 6 28 3 0.0 1 1 2 30 6 0.0 1 1 5 31 1 0.0 1 0 1 32 6 0.0 1 1 5 33 1 0.0 1 0 1 35 1 0.0 1 0 1 36 5 0.0 1 1 4 37 3 0.0 1 0 3 38 1 0.0 1 0 1 39 1 0.0 1 0 1 40 1 0.0 1 0 1 42 1 0.0 1 1 43 1 0.0 1 0 1 44 1 0.0 1 0 1 45 4 0.0 1 0 4 46 1 0.0 1 0 1 48 3 0.0 1 0 3 49 1 0.0 1 1 50 1 0.0 1 0 1 51 1 0.0 1 0 1 52 8 0.0 1 2 6 53 2 0.0 1 0 2 54 2 0.0 1 0 2 56 2 0.0 1 0 2 57 2 0.0 1 0 2 58 2 0.0 1 1 1 61 1 0.0 1 1 62 1 0.0 1 0 1 64 1 0.0 1 1 66 2 0.0 1 0 2 67 1 0.0 1 0 1 68 1 0.0 1 0 1 69 1 0.0 1 0 1 70 2 0.0 1 0 2 74 1 0.0 1 0 1 75 3 0.0 1 2 1 76 3 0.0 1 1 2 77 2 0.0 1 0 2 78 1 0.0 1 0 1 79 1 0.0 1 0 1 82 1 0.0 1 0 1 83 1 0.0 1 0 1 85 1 0.0 1 1 88 1 0.0 1 0 1 90 1 0.0 1 0 1 92 1 0.0 1 0 1 135 1 0.0 1 1 137 23 0.0 1 22 1 138 230 0.0 1 225 5 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041603_val_2.fq.gz ============================================= 85382 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2798 (3.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 85382 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 387 (0.45%)