SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041600_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/20201121/tmp/c30fca76-3f65-11eb-a036-6c92bfc06fea/trimmed/RRBS20A041600_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 553.45 s (39 us/read; 1.55 M reads/minute). === Summary === Total reads processed: 14,306,385 Reads with adapters: 5,464,043 (38.2%) Reads written (passing filters): 14,306,385 (100.0%) Total basepairs processed: 1,450,454,195 bp Total written (filtered): 1,358,664,385 bp (93.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5464043 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 57.3% G: 1.1% T: 7.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4747280 3576596.2 0 4747280 2 58769 894149.1 0 58769 3 11903 223537.3 0 11903 4 3342 55884.3 0 3342 5 869 13971.1 0 869 6 233 3492.8 0 233 7 808 873.2 0 808 8 665 218.3 0 665 9 185 54.6 0 171 14 10 1802 13.6 1 781 1021 11 117 3.4 1 40 77 12 1032 0.9 1 242 790 13 1758 0.2 1 411 1347 14 163 0.2 1 11 152 15 81 0.2 1 6 75 16 49 0.2 1 2 47 17 109 0.2 1 5 104 18 61 0.2 1 2 59 19 150 0.2 1 21 129 20 116 0.2 1 14 102 21 25 0.2 1 7 18 22 93 0.2 1 10 83 23 156 0.2 1 12 144 24 338 0.2 1 20 318 25 122 0.2 1 7 115 26 194 0.2 1 12 182 27 81 0.2 1 10 71 28 159 0.2 1 12 147 29 11 0.2 1 1 10 30 101 0.2 1 6 95 31 143 0.2 1 12 131 32 129 0.2 1 6 123 33 279 0.2 1 14 265 34 84 0.2 1 8 76 35 140 0.2 1 11 129 36 25 0.2 1 0 25 37 126 0.2 1 11 115 38 43 0.2 1 2 41 39 72 0.2 1 4 68 40 68 0.2 1 4 64 41 249 0.2 1 3 246 42 122 0.2 1 11 111 43 64 0.2 1 9 55 44 105 0.2 1 5 100 45 186 0.2 1 12 174 46 93 0.2 1 1 92 47 38 0.2 1 5 33 48 132 0.2 1 7 125 49 68 0.2 1 5 63 50 81 0.2 1 4 77 51 140 0.2 1 13 127 52 163 0.2 1 15 148 53 31 0.2 1 1 30 54 83 0.2 1 7 76 55 71 0.2 1 7 64 56 15 0.2 1 0 15 57 60 0.2 1 7 53 58 130 0.2 1 15 115 59 87 0.2 1 21 66 60 158 0.2 1 57 101 61 339 0.2 1 200 139 62 667 0.2 1 495 172 63 398 0.2 1 260 138 64 118 0.2 1 66 52 65 76 0.2 1 20 56 66 135 0.2 1 21 114 67 114 0.2 1 17 97 68 98 0.2 1 16 82 69 114 0.2 1 17 97 70 110 0.2 1 24 86 71 111 0.2 1 23 88 72 151 0.2 1 22 129 73 133 0.2 1 12 121 74 161 0.2 1 10 151 75 206 0.2 1 12 194 76 197 0.2 1 4 193 77 174 0.2 1 1 173 78 168 0.2 1 8 160 79 141 0.2 1 4 137 80 89 0.2 1 6 83 81 37 0.2 1 2 35 82 67 0.2 1 5 62 83 90 0.2 1 9 81 84 88 0.2 1 6 82 85 85 0.2 1 7 78 86 38 0.2 1 3 35 87 35 0.2 1 4 31 88 50 0.2 1 6 44 89 27 0.2 1 2 25 90 32 0.2 1 2 30 91 32 0.2 1 1 31 92 33 0.2 1 1 32 93 38 0.2 1 5 33 94 49 0.2 1 5 44 95 24 0.2 1 2 22 96 41 0.2 1 1 40 97 43 0.2 1 2 41 98 34 0.2 1 5 29 99 43 0.2 1 3 40 100 38 0.2 1 4 34 101 25 0.2 1 1 24 102 47 0.2 1 5 42 103 16 0.2 1 0 16 104 11 0.2 1 1 10 105 14 0.2 1 1 13 106 9 0.2 1 0 9 107 4 0.2 1 1 3 108 6 0.2 1 0 6 109 12 0.2 1 4 8 110 7 0.2 1 2 5 111 10 0.2 1 6 4 112 2 0.2 1 1 1 113 9 0.2 1 7 2 114 7 0.2 1 3 4 115 11 0.2 1 9 2 116 18 0.2 1 9 9 117 10 0.2 1 6 4 118 9 0.2 1 8 1 119 6 0.2 1 6 120 13 0.2 1 10 3 121 7 0.2 1 4 3 122 4 0.2 1 4 123 17 0.2 1 15 2 124 16 0.2 1 14 2 125 21 0.2 1 21 126 59 0.2 1 54 5 127 56 0.2 1 53 3 128 103 0.2 1 96 7 129 99 0.2 1 92 7 130 87 0.2 1 75 12 131 91 0.2 1 81 10 132 116 0.2 1 106 10 133 163 0.2 1 136 27 134 218 0.2 1 203 15 135 613 0.2 1 567 46 136 1311 0.2 1 1214 97 137 13455 0.2 1 12949 506 138 608780 0.2 1 599455 9325 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041600_val_2.fq.gz ============================================= 14306385 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 688421 (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: 14306385 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 674239 (4.71%)