SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041593_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/5f4d1d8a-48bc-11eb-bbaa-6c92bfc12b72/trimmed/RRBS20A041593_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 228.30 s (23 us/read; 2.64 M reads/minute). === Summary === Total reads processed: 10,050,107 Reads with adapters: 3,616,213 (36.0%) Reads written (passing filters): 10,050,107 (100.0%) Total basepairs processed: 949,592,888 bp Total written (filtered): 940,286,997 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3616213 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.2% C: 76.5% G: 2.0% T: 5.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3503679 2512526.8 0 3503679 2 50223 628131.7 0 50223 3 6585 157032.9 0 6585 4 2996 39258.2 0 2996 5 990 9814.6 0 990 6 361 2453.6 0 361 7 660 613.4 0 660 8 235 153.4 0 235 9 150 38.3 0 126 24 10 1205 9.6 1 279 926 11 112 2.4 1 17 95 12 1052 0.6 1 158 894 13 237 0.1 1 28 209 14 216 0.1 1 18 198 15 94 0.1 1 6 88 16 143 0.1 1 9 134 17 140 0.1 1 14 126 18 80 0.1 1 4 76 19 181 0.1 1 15 166 20 155 0.1 1 10 145 21 16 0.1 1 2 14 22 112 0.1 1 8 104 23 139 0.1 1 10 129 24 265 0.1 1 19 246 25 136 0.1 1 3 133 26 162 0.1 1 8 154 27 104 0.1 1 11 93 28 178 0.1 1 14 164 29 13 0.1 1 1 12 30 169 0.1 1 10 159 31 145 0.1 1 12 133 32 168 0.1 1 10 158 33 360 0.1 1 18 342 34 107 0.1 1 3 104 35 193 0.1 1 12 181 36 41 0.1 1 2 39 37 194 0.1 1 12 182 38 97 0.1 1 6 91 39 115 0.1 1 5 110 40 116 0.1 1 9 107 41 86 0.1 1 3 83 42 127 0.1 1 8 119 43 102 0.1 1 6 96 44 166 0.1 1 12 154 45 205 0.1 1 9 196 46 161 0.1 1 12 149 47 119 0.1 1 8 111 48 211 0.1 1 8 203 49 139 0.1 1 8 131 50 139 0.1 1 8 131 51 178 0.1 1 11 167 52 194 0.1 1 11 183 53 36 0.1 1 2 34 54 127 0.1 1 8 119 55 135 0.1 1 10 125 56 26 0.1 1 0 26 57 112 0.1 1 4 108 58 189 0.1 1 14 175 59 106 0.1 1 9 97 60 173 0.1 1 12 161 61 184 0.1 1 21 163 62 296 0.1 1 20 276 63 310 0.1 1 33 277 64 144 0.1 1 4 140 65 144 0.1 1 10 134 66 313 0.1 1 36 277 67 122 0.1 1 5 117 68 126 0.1 1 7 119 69 118 0.1 1 7 111 70 100 0.1 1 8 92 71 105 0.1 1 11 94 72 117 0.1 1 7 110 73 133 0.1 1 5 128 74 119 0.1 1 8 111 75 182 0.1 1 11 171 76 174 0.1 1 5 169 77 182 0.1 1 12 170 78 129 0.1 1 4 125 79 130 0.1 1 5 125 80 106 0.1 1 4 102 81 84 0.1 1 1 83 82 109 0.1 1 10 99 83 95 0.1 1 6 89 84 122 0.1 1 7 115 85 136 0.1 1 10 126 86 79 0.1 1 7 72 87 61 0.1 1 4 57 88 76 0.1 1 3 73 89 52 0.1 1 2 50 90 44 0.1 1 3 41 91 53 0.1 1 5 48 92 43 0.1 1 4 39 93 48 0.1 1 1 47 94 85 0.1 1 4 81 95 36 0.1 1 2 34 96 57 0.1 1 10 47 97 64 0.1 1 7 57 98 40 0.1 1 6 34 99 39 0.1 1 6 33 100 42 0.1 1 2 40 101 28 0.1 1 2 26 102 54 0.1 1 3 51 103 18 0.1 1 1 17 104 19 0.1 1 0 19 105 16 0.1 1 0 16 106 12 0.1 1 2 10 107 5 0.1 1 0 5 108 6 0.1 1 1 5 109 12 0.1 1 4 8 110 14 0.1 1 0 14 112 1 0.1 1 1 113 1 0.1 1 0 1 114 4 0.1 1 1 3 115 2 0.1 1 0 2 116 2 0.1 1 0 2 117 2 0.1 1 2 118 3 0.1 1 2 1 121 1 0.1 1 1 123 1 0.1 1 1 126 1 0.1 1 1 127 4 0.1 1 2 2 128 5 0.1 1 5 129 8 0.1 1 6 2 130 4 0.1 1 3 1 131 9 0.1 1 6 3 132 5 0.1 1 4 1 133 15 0.1 1 14 1 134 9 0.1 1 6 3 135 30 0.1 1 24 6 136 112 0.1 1 109 3 137 3617 0.1 1 3521 96 138 27446 0.1 1 26750 696 139 5093 0.1 1 0 5093 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041593_val_2.fq.gz ============================================= 10050107 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 625663 (6.2%) 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: 10050107 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 75398 (0.75%)