SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041624_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/c364d976-3f65-11eb-8174-b4055d0383c6/trimmed/RRBS20A041624_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 258.84 s (27 us/read; 2.19 M reads/minute). === Summary === Total reads processed: 9,468,826 Reads with adapters: 3,178,181 (33.6%) Reads written (passing filters): 9,468,826 (100.0%) Total basepairs processed: 912,620,259 bp Total written (filtered): 892,436,471 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3178181 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.9% C: 73.9% G: 0.7% T: 5.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3015553 2367206.5 0 3015553 2 22546 591801.6 0 22546 3 4565 147950.4 0 4565 4 2767 36987.6 0 2767 5 881 9246.9 0 881 6 261 2311.7 0 261 7 409 577.9 0 409 8 217 144.5 0 217 9 192 36.1 0 171 21 10 1289 9.0 1 283 1006 11 88 2.3 1 35 53 12 147 0.6 1 41 106 13 31 0.1 1 5 26 14 187 0.1 1 13 174 15 87 0.1 1 3 84 16 115 0.1 1 5 110 17 128 0.1 1 6 122 18 78 0.1 1 2 76 19 188 0.1 1 9 179 20 150 0.1 1 12 138 21 14 0.1 1 0 14 22 43 0.1 1 4 39 23 159 0.1 1 7 152 24 398 0.1 1 45 353 25 156 0.1 1 8 148 26 197 0.1 1 13 184 27 86 0.1 1 5 81 28 127 0.1 1 10 117 29 15 0.1 1 1 14 30 35 0.1 1 1 34 31 114 0.1 1 7 107 32 188 0.1 1 8 180 33 329 0.1 1 24 305 34 68 0.1 1 4 64 35 80 0.1 1 10 70 36 22 0.1 1 1 21 37 155 0.1 1 8 147 38 54 0.1 1 3 51 39 78 0.1 1 5 73 40 84 0.1 1 2 82 41 64 0.1 1 2 62 42 126 0.1 1 5 121 43 59 0.1 1 5 54 44 117 0.1 1 5 112 45 201 0.1 1 14 187 46 123 0.1 1 8 115 47 43 0.1 1 3 40 48 149 0.1 1 9 140 49 100 0.1 1 5 95 50 112 0.1 1 8 104 51 167 0.1 1 14 153 52 201 0.1 1 22 179 53 20 0.1 1 2 18 54 98 0.1 1 2 96 55 88 0.1 1 5 83 56 18 0.1 1 1 17 57 80 0.1 1 2 78 58 168 0.1 1 8 160 59 88 0.1 1 11 77 60 115 0.1 1 13 102 61 145 0.1 1 12 133 62 181 0.1 1 27 154 63 137 0.1 1 10 127 64 65 0.1 1 0 65 65 65 0.1 1 5 60 66 183 0.1 1 10 173 67 110 0.1 1 8 102 68 80 0.1 1 11 69 69 66 0.1 1 2 64 70 78 0.1 1 6 72 71 64 0.1 1 2 62 72 67 0.1 1 11 56 73 72 0.1 1 4 68 74 84 0.1 1 6 78 75 167 0.1 1 20 147 76 94 0.1 1 6 88 77 86 0.1 1 5 81 78 98 0.1 1 4 94 79 74 0.1 1 10 64 80 92 0.1 1 7 85 81 67 0.1 1 3 64 82 75 0.1 1 7 68 83 70 0.1 1 2 68 84 120 0.1 1 5 115 85 75 0.1 1 4 71 86 65 0.1 1 6 59 87 44 0.1 1 5 39 88 52 0.1 1 3 49 89 33 0.1 1 2 31 90 37 0.1 1 0 37 91 33 0.1 1 2 31 92 25 0.1 1 3 22 93 46 0.1 1 2 44 94 65 0.1 1 5 60 95 35 0.1 1 3 32 96 27 0.1 1 1 26 97 30 0.1 1 0 30 98 27 0.1 1 3 24 99 41 0.1 1 3 38 100 44 0.1 1 5 39 101 30 0.1 1 2 28 102 41 0.1 1 2 39 103 19 0.1 1 0 19 104 13 0.1 1 0 13 105 6 0.1 1 0 6 106 10 0.1 1 2 8 107 6 0.1 1 1 5 108 6 0.1 1 0 6 109 7 0.1 1 1 6 110 7 0.1 1 1 6 112 1 0.1 1 1 116 1 0.1 1 1 121 1 0.1 1 1 124 2 0.1 1 1 1 126 5 0.1 1 2 3 127 4 0.1 1 4 128 7 0.1 1 7 129 8 0.1 1 7 1 130 6 0.1 1 5 1 131 4 0.1 1 3 1 132 5 0.1 1 5 133 7 0.1 1 5 2 134 18 0.1 1 14 4 135 42 0.1 1 36 6 136 192 0.1 1 174 18 137 13864 0.1 1 13580 284 138 103628 0.1 1 101166 2462 139 2804 0.1 1 0 2804 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041624_val_2.fq.gz ============================================= 9468826 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 504718 (5.3%) 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: 9468826 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 152197 (1.61%)