SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041598_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/20201104_20201106/tmp/5f253f18-48bc-11eb-991a-b4055d0383c6/trimmed/RRBS20A041598_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1087.14 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 44,705,946 Reads with adapters: 18,835,852 (42.1%) Reads written (passing filters): 44,705,946 (100.0%) Total basepairs processed: 4,545,435,092 bp Total written (filtered): 4,498,132,418 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18835852 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.9% C: 1.8% G: 19.4% T: 47.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13702858 11176486.5 0 13702858 2 3793108 2794121.6 0 3793108 3 848924 698530.4 0 848924 4 190600 174632.6 0 190600 5 10738 43658.2 0 10738 6 5342 10914.5 0 5342 7 3326 2728.6 0 3326 8 2820 682.2 0 2820 9 4284 170.5 0 3646 638 10 5624 42.6 1 1652 3972 11 3670 10.7 1 520 3150 12 1462 2.7 1 194 1268 13 1414 0.7 1 174 1240 14 2836 0.7 1 350 2486 15 2650 0.7 1 324 2326 16 6348 0.7 1 926 5422 17 7800 0.7 1 1012 6788 18 3002 0.7 1 410 2592 19 182 0.7 1 12 170 20 1576 0.7 1 194 1382 21 150 0.7 1 14 136 22 206 0.7 1 18 188 23 1562 0.7 1 194 1368 24 4206 0.7 1 584 3622 25 2424 0.7 1 438 1986 26 622 0.7 1 90 532 27 2328 0.7 1 314 2014 28 4342 0.7 1 646 3696 29 4044 0.7 1 576 3468 30 1202 0.7 1 180 1022 31 360 0.7 1 40 320 32 2492 0.7 1 332 2160 33 3150 0.7 1 464 2686 34 3894 0.7 1 522 3372 35 2440 0.7 1 324 2116 36 1830 0.7 1 226 1604 37 3088 0.7 1 394 2694 38 698 0.7 1 78 620 39 358 0.7 1 40 318 40 2320 0.7 1 274 2046 41 1216 0.7 1 126 1090 42 2542 0.7 1 334 2208 43 4286 0.7 1 552 3734 44 744 0.7 1 96 648 45 2388 0.7 1 352 2036 46 740 0.7 1 68 672 47 1632 0.7 1 178 1454 48 3670 0.7 1 538 3132 49 500 0.7 1 70 430 50 1948 0.7 1 276 1672 51 680 0.7 1 102 578 52 670 0.7 1 106 564 53 1886 0.7 1 290 1596 54 5878 0.7 1 734 5144 55 2682 0.7 1 356 2326 56 1672 0.7 1 196 1476 57 2628 0.7 1 366 2262 58 1562 0.7 1 210 1352 59 908 0.7 1 110 798 60 1600 0.7 1 182 1418 61 2462 0.7 1 314 2148 62 4526 0.7 1 628 3898 63 1278 0.7 1 150 1128 64 146 0.7 1 14 132 65 134 0.7 1 10 124 66 670 0.7 1 56 614 67 618 0.7 1 66 552 68 1854 0.7 1 240 1614 69 1912 0.7 1 238 1674 70 3376 0.7 1 450 2926 71 1466 0.7 1 164 1302 72 538 0.7 1 38 500 73 746 0.7 1 70 676 74 500 0.7 1 66 434 75 620 0.7 1 64 556 76 714 0.7 1 88 626 77 744 0.7 1 96 648 78 794 0.7 1 90 704 79 834 0.7 1 86 748 80 1108 0.7 1 158 950 81 836 0.7 1 106 730 82 1092 0.7 1 148 944 83 884 0.7 1 110 774 84 722 0.7 1 86 636 85 768 0.7 1 94 674 86 912 0.7 1 108 804 87 572 0.7 1 82 490 88 518 0.7 1 56 462 89 680 0.7 1 90 590 90 496 0.7 1 54 442 91 426 0.7 1 54 372 92 502 0.7 1 38 464 93 2720 0.7 1 252 2468 94 4078 0.7 1 404 3674 95 886 0.7 1 88 798 96 516 0.7 1 62 454 97 3334 0.7 1 448 2886 98 422 0.7 1 60 362 99 254 0.7 1 26 228 100 272 0.7 1 26 246 101 312 0.7 1 48 264 102 654 0.7 1 148 506 103 208 0.7 1 36 172 104 114 0.7 1 16 98 105 150 0.7 1 22 128 106 132 0.7 1 22 110 107 72 0.7 1 22 50 108 18 0.7 1 2 16 109 64 0.7 1 2 62 110 300 0.7 1 76 224 111 4 0.7 1 2 2 114 4 0.7 1 0 4 119 4 0.7 1 0 4 125 2 0.7 1 2 126 2 0.7 1 0 2 130 4 0.7 1 2 2 131 6 0.7 1 4 2 132 16 0.7 1 8 8 133 32 0.7 1 16 16 134 30 0.7 1 28 2 135 40 0.7 1 36 4 136 90 0.7 1 70 20 137 3894 0.7 1 3764 130 138 103642 0.7 1 100322 3320 140 16 0.7 1 0 16 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041598_val_1.fq.gz ============================================= 44705946 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2074100 (4.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18835844 (42.1%)