SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041623_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/processing/cup/BS_workflow/20201104_20201106/tmp/5f253770-48bc-11eb-adb9-b4055d0383c6/trimmed/RRBS20A041623_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 2.62 s (23 us/read; 2.61 M reads/minute). === Summary === Total reads processed: 113,686 Reads with adapters: 40,100 (35.3%) Reads written (passing filters): 113,686 (100.0%) Total basepairs processed: 10,366,772 bp Total written (filtered): 10,273,156 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40100 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 13.9% C: 81.3% G: 0.7% T: 4.1% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 38602 28421.5 0 38602 2 472 7105.4 0 472 3 108 1776.3 0 108 4 48 444.1 0 48 5 34 111.0 0 34 6 20 27.8 0 20 7 10 6.9 0 10 8 16 1.7 0 16 9 12 0.4 0 12 10 30 0.1 1 10 20 11 6 0.0 1 2 4 12 6 0.0 1 0 6 13 10 0.0 1 0 10 14 10 0.0 1 0 10 15 4 0.0 1 2 2 16 6 0.0 1 0 6 17 10 0.0 1 2 8 18 10 0.0 1 2 8 19 8 0.0 1 2 6 20 6 0.0 1 0 6 23 8 0.0 1 0 8 24 20 0.0 1 2 18 25 6 0.0 1 2 4 26 16 0.0 1 4 12 27 2 0.0 1 0 2 28 6 0.0 1 2 4 29 4 0.0 1 0 4 30 2 0.0 1 0 2 31 6 0.0 1 4 2 32 4 0.0 1 0 4 33 22 0.0 1 4 18 35 4 0.0 1 2 2 36 2 0.0 1 0 2 37 4 0.0 1 2 2 38 2 0.0 1 0 2 39 6 0.0 1 0 6 40 8 0.0 1 0 8 41 8 0.0 1 0 8 42 2 0.0 1 0 2 43 10 0.0 1 0 10 44 4 0.0 1 0 4 45 4 0.0 1 4 46 8 0.0 1 0 8 47 6 0.0 1 0 6 48 8 0.0 1 4 4 49 4 0.0 1 0 4 50 10 0.0 1 4 6 51 12 0.0 1 4 8 52 10 0.0 1 2 8 54 10 0.0 1 0 10 55 12 0.0 1 0 12 56 2 0.0 1 0 2 57 8 0.0 1 0 8 58 8 0.0 1 4 4 59 8 0.0 1 2 6 60 10 0.0 1 0 10 61 10 0.0 1 2 8 62 22 0.0 1 0 22 63 26 0.0 1 4 22 64 8 0.0 1 0 8 65 6 0.0 1 0 6 66 20 0.0 1 2 18 67 6 0.0 1 0 6 68 2 0.0 1 0 2 69 8 0.0 1 0 8 70 2 0.0 1 2 71 8 0.0 1 0 8 72 4 0.0 1 0 4 73 8 0.0 1 2 6 75 2 0.0 1 0 2 76 10 0.0 1 2 8 77 4 0.0 1 2 2 78 6 0.0 1 0 6 79 4 0.0 1 0 4 80 6 0.0 1 0 6 81 6 0.0 1 2 4 82 4 0.0 1 0 4 83 2 0.0 1 0 2 84 8 0.0 1 2 6 85 12 0.0 1 0 12 86 4 0.0 1 0 4 87 4 0.0 1 0 4 88 6 0.0 1 2 4 89 4 0.0 1 0 4 90 2 0.0 1 0 2 92 2 0.0 1 0 2 94 4 0.0 1 0 4 95 4 0.0 1 0 4 97 2 0.0 1 0 2 99 4 0.0 1 0 4 100 2 0.0 1 0 2 101 8 0.0 1 2 6 102 2 0.0 1 0 2 103 2 0.0 1 0 2 105 4 0.0 1 0 4 106 2 0.0 1 0 2 107 2 0.0 1 0 2 137 10 0.0 1 10 138 144 0.0 1 142 2 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041623_val_2.fq.gz ============================================= 113686 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7616 (6.7%) 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: 113686 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 646 (0.57%)