SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041689_val_1.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/20201110/tmp/cd67b24a-5581-11eb-85e4-6c92bfc12bba/trimmed/RRBS20A041689_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 181.13 s (24 us/read; 2.48 M reads/minute). === Summary === Total reads processed: 7,481,333 Reads with adapters: 3,124,607 (41.8%) Reads written (passing filters): 7,481,333 (100.0%) Total basepairs processed: 770,409,075 bp Total written (filtered): 730,851,313 bp (94.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3124607 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.8% C: 9.3% G: 18.7% T: 45.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2101767 1870333.2 0 2101767 2 586990 467583.3 0 586990 3 125463 116895.8 0 125463 4 29004 29224.0 0 29004 5 1509 7306.0 0 1509 6 638 1826.5 0 638 7 436 456.6 0 436 8 336 114.2 0 336 9 703 28.5 0 635 68 10 645 7.1 1 195 450 11 537 1.8 1 58 479 12 176 0.4 1 20 156 13 204 0.1 1 29 175 14 502 0.1 1 64 438 15 517 0.1 1 105 412 16 1555 0.1 1 445 1110 17 1564 0.1 1 227 1337 18 360 0.1 1 59 301 19 28 0.1 1 5 23 20 213 0.1 1 27 186 21 30 0.1 1 1 29 22 46 0.1 1 6 40 23 233 0.1 1 36 197 24 863 0.1 1 148 715 25 311 0.1 1 48 263 26 99 0.1 1 15 84 27 317 0.1 1 39 278 28 765 0.1 1 122 643 29 784 0.1 1 107 677 30 97 0.1 1 10 87 31 20 0.1 1 0 20 32 220 0.1 1 27 193 33 511 0.1 1 75 436 34 465 0.1 1 64 401 35 836 0.1 1 114 722 36 378 0.1 1 55 323 37 116 0.1 1 16 100 38 515 0.1 1 87 428 39 168 0.1 1 26 142 40 780 0.1 1 118 662 41 413 0.1 1 50 363 42 546 0.1 1 80 466 43 622 0.1 1 84 538 44 154 0.1 1 17 137 45 403 0.1 1 50 353 46 113 0.1 1 13 100 47 244 0.1 1 30 214 48 721 0.1 1 112 609 49 148 0.1 1 19 129 50 287 0.1 1 37 250 51 152 0.1 1 21 131 52 88 0.1 1 10 78 53 223 0.1 1 36 187 54 763 0.1 1 91 672 55 344 0.1 1 42 302 56 248 0.1 1 28 220 57 275 0.1 1 43 232 58 166 0.1 1 19 147 59 131 0.1 1 12 119 60 153 0.1 1 19 134 61 251 0.1 1 29 222 62 545 0.1 1 102 443 63 135 0.1 1 23 112 64 24 0.1 1 4 20 65 16 0.1 1 2 14 66 80 0.1 1 10 70 67 77 0.1 1 9 68 68 289 0.1 1 43 246 69 320 0.1 1 36 284 70 438 0.1 1 48 390 71 125 0.1 1 13 112 72 39 0.1 1 6 33 73 43 0.1 1 9 34 74 49 0.1 1 8 41 75 73 0.1 1 14 59 76 98 0.1 1 15 83 77 144 0.1 1 17 127 78 156 0.1 1 27 129 79 124 0.1 1 19 105 80 189 0.1 1 26 163 81 115 0.1 1 14 101 82 199 0.1 1 20 179 83 141 0.1 1 21 120 84 105 0.1 1 13 92 85 102 0.1 1 11 91 86 182 0.1 1 15 167 87 124 0.1 1 21 103 88 96 0.1 1 18 78 89 95 0.1 1 15 80 90 88 0.1 1 10 78 91 83 0.1 1 8 75 92 91 0.1 1 18 73 93 483 0.1 1 63 420 94 995 0.1 1 149 846 95 192 0.1 1 24 168 96 82 0.1 1 15 67 97 768 0.1 1 117 651 98 97 0.1 1 24 73 99 43 0.1 1 9 34 100 54 0.1 1 8 46 101 46 0.1 1 8 38 102 109 0.1 1 21 88 103 31 0.1 1 4 27 104 25 0.1 1 4 21 105 22 0.1 1 3 19 106 25 0.1 1 1 24 107 11 0.1 1 1 10 108 9 0.1 1 2 7 109 7 0.1 1 0 7 110 36 0.1 1 8 28 111 4 0.1 1 2 2 112 3 0.1 1 0 3 114 6 0.1 1 2 4 117 2 0.1 1 2 120 1 0.1 1 0 1 121 5 0.1 1 2 3 122 1 0.1 1 1 124 3 0.1 1 3 125 4 0.1 1 3 1 126 4 0.1 1 3 1 127 3 0.1 1 2 1 128 1 0.1 1 1 129 7 0.1 1 7 130 5 0.1 1 4 1 131 16 0.1 1 12 4 132 27 0.1 1 26 1 133 46 0.1 1 35 11 134 90 0.1 1 74 16 135 68 0.1 1 61 7 136 178 0.1 1 152 26 137 11383 0.1 1 10980 403 138 238181 0.1 1 232111 6070 140 3 0.1 1 0 3 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041689_val_1.fq.gz ============================================= 7481333 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 285571 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 3124597 (41.8%)