SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041583_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/6028bc46-48bc-11eb-95f7-6c92bfc12bd2/trimmed/RRBS20A041583_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 283.98 s (22 us/read; 2.69 M reads/minute). === Summary === Total reads processed: 12,744,424 Reads with adapters: 4,394,974 (34.5%) Reads written (passing filters): 12,744,424 (100.0%) Total basepairs processed: 1,246,839,579 bp Total written (filtered): 1,238,825,656 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4394974 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.8% C: 73.3% G: 1.5% T: 6.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4316364 3186106.0 0 4316364 2 36425 796526.5 0 36425 3 5131 199131.6 0 5131 4 2159 49782.9 0 2159 5 736 12445.7 0 736 6 270 3111.4 0 270 7 599 777.9 0 599 8 179 194.5 0 179 9 111 48.6 0 97 14 10 935 12.2 1 186 749 11 54 3.0 1 4 50 12 872 0.8 1 99 773 13 145 0.2 1 7 138 14 153 0.2 1 5 148 15 50 0.2 1 3 47 16 92 0.2 1 7 85 17 119 0.2 1 5 114 18 54 0.2 1 3 51 19 158 0.2 1 9 149 20 121 0.2 1 5 116 21 6 0.2 1 0 6 22 97 0.2 1 8 89 23 122 0.2 1 9 113 24 354 0.2 1 22 332 25 112 0.2 1 7 105 26 179 0.2 1 10 169 27 75 0.2 1 2 73 28 171 0.2 1 9 162 29 20 0.2 1 1 19 30 108 0.2 1 8 100 31 95 0.2 1 6 89 32 143 0.2 1 4 139 33 270 0.2 1 13 257 34 57 0.2 1 3 54 35 171 0.2 1 10 161 36 28 0.2 1 1 27 37 179 0.2 1 7 172 38 57 0.2 1 3 54 39 92 0.2 1 4 88 40 68 0.2 1 3 65 41 71 0.2 1 4 67 42 139 0.2 1 4 135 43 80 0.2 1 7 73 44 109 0.2 1 9 100 45 194 0.2 1 15 179 46 122 0.2 1 1 121 47 61 0.2 1 7 54 48 180 0.2 1 10 170 49 92 0.2 1 6 86 50 113 0.2 1 5 108 51 119 0.2 1 4 115 52 182 0.2 1 6 176 53 13 0.2 1 2 11 54 89 0.2 1 0 89 55 85 0.2 1 4 81 56 15 0.2 1 2 13 57 66 0.2 1 5 61 58 145 0.2 1 8 137 59 65 0.2 1 4 61 60 99 0.2 1 7 92 61 118 0.2 1 9 109 62 158 0.2 1 20 138 63 139 0.2 1 12 127 64 68 0.2 1 5 63 65 52 0.2 1 1 51 66 152 0.2 1 11 141 67 80 0.2 1 3 77 68 68 0.2 1 5 63 69 68 0.2 1 6 62 70 66 0.2 1 3 63 71 79 0.2 1 4 75 72 73 0.2 1 7 66 73 72 0.2 1 1 71 74 98 0.2 1 1 97 75 162 0.2 1 9 153 76 176 0.2 1 8 168 77 122 0.2 1 3 119 78 80 0.2 1 0 80 79 92 0.2 1 3 89 80 74 0.2 1 3 71 81 60 0.2 1 3 57 82 78 0.2 1 5 73 83 64 0.2 1 7 57 84 88 0.2 1 4 84 85 81 0.2 1 6 75 86 51 0.2 1 2 49 87 48 0.2 1 4 44 88 40 0.2 1 1 39 89 38 0.2 1 4 34 90 28 0.2 1 1 27 91 29 0.2 1 1 28 92 27 0.2 1 1 26 93 38 0.2 1 1 37 94 33 0.2 1 1 32 95 31 0.2 1 5 26 96 13 0.2 1 0 13 97 34 0.2 1 3 31 98 17 0.2 1 2 15 99 19 0.2 1 1 18 100 21 0.2 1 1 20 101 12 0.2 1 1 11 102 18 0.2 1 0 18 103 11 0.2 1 0 11 104 9 0.2 1 3 6 105 12 0.2 1 0 12 106 5 0.2 1 0 5 107 7 0.2 1 1 6 108 9 0.2 1 3 6 109 20 0.2 1 2 18 110 6 0.2 1 0 6 111 2 0.2 1 1 1 112 1 0.2 1 0 1 113 1 0.2 1 0 1 114 1 0.2 1 0 1 115 1 0.2 1 0 1 120 1 0.2 1 0 1 122 1 0.2 1 1 123 1 0.2 1 1 126 2 0.2 1 1 1 127 1 0.2 1 1 128 1 0.2 1 1 129 3 0.2 1 3 131 1 0.2 1 1 132 4 0.2 1 3 1 133 5 0.2 1 4 1 134 5 0.2 1 4 1 135 8 0.2 1 7 1 136 62 0.2 1 57 5 137 2733 0.2 1 2684 49 138 17110 0.2 1 16846 264 139 2916 0.2 1 0 2916 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041583_val_2.fq.gz ============================================= 12744424 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 612665 (4.8%) 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: 12744424 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 56615 (0.44%)