SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041685_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/ab50e80e-3dd8-11eb-bd4d-6c92bfc12c98/trimmed/RRBS20A041685_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 2.09 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 101,608 Reads with adapters: 30,054 (29.6%) Reads written (passing filters): 101,608 (100.0%) Total basepairs processed: 10,222,725 bp Total written (filtered): 10,139,791 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30054 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.9% C: 70.2% G: 1.1% T: 8.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29308 25402.0 0 29308 2 192 6350.5 0 192 3 25 1587.6 0 25 4 13 396.9 0 13 5 7 99.2 0 7 6 4 24.8 0 4 7 7 6.2 0 7 8 6 1.6 0 6 9 3 0.4 0 3 10 9 0.1 1 2 7 11 1 0.0 1 1 12 13 0.0 1 5 8 13 5 0.0 1 1 4 14 4 0.0 1 1 3 15 2 0.0 1 0 2 16 1 0.0 1 0 1 17 2 0.0 1 0 2 18 1 0.0 1 1 19 4 0.0 1 2 2 20 1 0.0 1 0 1 22 2 0.0 1 0 2 23 2 0.0 1 0 2 24 11 0.0 1 1 10 25 1 0.0 1 0 1 26 6 0.0 1 0 6 27 1 0.0 1 0 1 28 3 0.0 1 1 2 30 3 0.0 1 1 2 31 2 0.0 1 1 1 32 2 0.0 1 0 2 33 2 0.0 1 0 2 34 1 0.0 1 0 1 35 1 0.0 1 1 37 2 0.0 1 1 1 38 2 0.0 1 0 2 39 1 0.0 1 0 1 41 3 0.0 1 0 3 42 1 0.0 1 0 1 43 1 0.0 1 0 1 44 2 0.0 1 0 2 45 2 0.0 1 0 2 48 6 0.0 1 0 6 50 1 0.0 1 0 1 51 1 0.0 1 0 1 52 2 0.0 1 1 1 53 1 0.0 1 0 1 54 2 0.0 1 0 2 55 2 0.0 1 0 2 56 2 0.0 1 1 1 57 3 0.0 1 0 3 58 1 0.0 1 0 1 59 1 0.0 1 0 1 61 1 0.0 1 1 62 1 0.0 1 0 1 65 2 0.0 1 0 2 66 1 0.0 1 0 1 68 1 0.0 1 0 1 69 1 0.0 1 0 1 70 1 0.0 1 0 1 71 2 0.0 1 0 2 73 1 0.0 1 0 1 74 1 0.0 1 0 1 75 3 0.0 1 0 3 76 4 0.0 1 0 4 81 1 0.0 1 0 1 82 2 0.0 1 0 2 83 1 0.0 1 0 1 84 1 0.0 1 0 1 87 2 0.0 1 0 2 89 1 0.0 1 0 1 92 1 0.0 1 0 1 94 2 0.0 1 0 2 137 9 0.0 1 8 1 138 334 0.0 1 332 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201028_merged/RRBS20A041685_val_2.fq.gz ============================================= 101608 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3771 (3.7%) 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: 101608 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 511 (0.50%)