SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041590_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/20201118/tmp/68c6048e-5592-11eb-8c03-6c92bfc12ff2/trimmed/RRBS20A041590_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 105.35 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 4,322,205 Reads with adapters: 1,780,681 (41.2%) Reads written (passing filters): 4,322,205 (100.0%) Total basepairs processed: 468,955,585 bp Total written (filtered): 465,764,025 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1780681 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.9% C: 70.6% G: 1.6% T: 6.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1745841 1080551.2 0 1745841 2 12954 270137.8 0 12954 3 2084 67534.5 0 2084 4 1259 16883.6 0 1259 5 422 4220.9 0 422 6 224 1055.2 0 224 7 365 263.8 0 365 8 199 66.0 0 199 9 115 16.5 0 109 6 10 818 4.1 1 194 624 11 39 1.0 1 5 34 12 659 0.3 1 146 513 13 180 0.1 1 13 167 14 284 0.1 1 36 248 15 95 0.1 1 12 83 16 114 0.1 1 10 104 17 303 0.1 1 31 272 18 92 0.1 1 8 84 19 278 0.1 1 22 256 20 186 0.1 1 20 166 21 6 0.1 1 0 6 22 162 0.1 1 17 145 23 191 0.1 1 13 178 24 479 0.1 1 32 447 25 146 0.1 1 6 140 26 256 0.1 1 31 225 27 105 0.1 1 8 97 28 157 0.1 1 16 141 29 18 0.1 1 0 18 30 168 0.1 1 12 156 31 164 0.1 1 21 143 32 145 0.1 1 8 137 33 373 0.1 1 50 323 34 116 0.1 1 8 108 35 180 0.1 1 12 168 36 30 0.1 1 3 27 37 154 0.1 1 18 136 38 39 0.1 1 4 35 39 70 0.1 1 10 60 40 41 0.1 1 5 36 41 85 0.1 1 9 76 42 139 0.1 1 12 127 43 55 0.1 1 8 47 44 83 0.1 1 7 76 45 238 0.1 1 19 219 46 77 0.1 1 8 69 47 28 0.1 1 2 26 48 128 0.1 1 18 110 49 78 0.1 1 3 75 50 136 0.1 1 16 120 51 149 0.1 1 14 135 52 141 0.1 1 13 128 53 21 0.1 1 1 20 54 85 0.1 1 10 75 55 57 0.1 1 5 52 56 11 0.1 1 0 11 57 53 0.1 1 5 48 58 129 0.1 1 13 116 59 66 0.1 1 3 63 60 98 0.1 1 9 89 61 106 0.1 1 8 98 62 132 0.1 1 20 112 63 108 0.1 1 10 98 64 35 0.1 1 9 26 65 32 0.1 1 2 30 66 73 0.1 1 8 65 67 66 0.1 1 9 57 68 57 0.1 1 3 54 69 52 0.1 1 6 46 70 53 0.1 1 6 47 71 60 0.1 1 3 57 72 35 0.1 1 2 33 73 46 0.1 1 6 40 74 35 0.1 1 4 31 75 62 0.1 1 4 58 76 74 0.1 1 7 67 77 65 0.1 1 6 59 78 22 0.1 1 0 22 79 35 0.1 1 4 31 80 34 0.1 1 2 32 81 43 0.1 1 2 41 82 48 0.1 1 8 40 83 33 0.1 1 8 25 84 30 0.1 1 3 27 85 47 0.1 1 4 43 86 27 0.1 1 4 23 87 23 0.1 1 6 17 88 22 0.1 1 3 19 89 16 0.1 1 0 16 90 13 0.1 1 1 12 91 11 0.1 1 0 11 92 21 0.1 1 5 16 93 25 0.1 1 2 23 94 27 0.1 1 2 25 95 17 0.1 1 2 15 96 17 0.1 1 2 15 97 13 0.1 1 0 13 98 18 0.1 1 4 14 99 9 0.1 1 0 9 100 14 0.1 1 2 12 101 5 0.1 1 1 4 102 9 0.1 1 3 6 103 8 0.1 1 0 8 104 9 0.1 1 2 7 105 3 0.1 1 0 3 106 2 0.1 1 0 2 107 2 0.1 1 1 1 108 1 0.1 1 0 1 109 2 0.1 1 1 1 110 8 0.1 1 1 7 115 1 0.1 1 0 1 133 1 0.1 1 1 134 1 0.1 1 1 136 2 0.1 1 2 137 204 0.1 1 199 5 138 7399 0.1 1 7261 138 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041590_val_2.fq.gz ============================================= 4322205 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 229535 (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: 4322205 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 13197 (0.31%)