SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041595_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/599cb8d2-48bc-11eb-9653-6c92bfbea1ec/trimmed/RRBS20A041595_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 689.94 s (22 us/read; 2.67 M reads/minute). === Summary === Total reads processed: 30,665,748 Reads with adapters: 13,000,518 (42.4%) Reads written (passing filters): 30,665,748 (100.0%) Total basepairs processed: 3,078,110,952 bp Total written (filtered): 3,049,414,422 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13000518 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 0.8% G: 20.5% T: 48.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9462752 7666437.0 0 9462752 2 2614978 1916609.2 0 2614978 3 585200 479152.3 0 585200 4 141618 119788.1 0 141618 5 7362 29947.0 0 7362 6 3512 7486.8 0 3512 7 1824 1871.7 0 1824 8 2020 467.9 0 2020 9 3364 117.0 0 3012 352 10 3266 29.2 1 952 2314 11 2642 7.3 1 398 2244 12 1148 1.8 1 166 982 13 1298 0.5 1 190 1108 14 2194 0.5 1 356 1838 15 1936 0.5 1 242 1694 16 4524 0.5 1 630 3894 17 6244 0.5 1 1062 5182 18 2466 0.5 1 474 1992 19 126 0.5 1 24 102 20 1362 0.5 1 208 1154 21 136 0.5 1 16 120 22 194 0.5 1 20 174 23 1428 0.5 1 198 1230 24 3512 0.5 1 660 2852 25 1896 0.5 1 418 1478 26 454 0.5 1 66 388 27 1920 0.5 1 252 1668 28 3444 0.5 1 526 2918 29 3230 0.5 1 506 2724 30 838 0.5 1 148 690 31 204 0.5 1 28 176 32 2070 0.5 1 316 1754 33 2444 0.5 1 400 2044 34 3122 0.5 1 476 2646 35 1844 0.5 1 252 1592 36 1630 0.5 1 284 1346 37 2766 0.5 1 476 2290 38 586 0.5 1 76 510 39 370 0.5 1 58 312 40 2094 0.5 1 362 1732 41 1634 0.5 1 264 1370 42 2420 0.5 1 472 1948 43 3972 0.5 1 650 3322 44 736 0.5 1 104 632 45 2322 0.5 1 458 1864 46 756 0.5 1 116 640 47 1644 0.5 1 278 1366 48 3342 0.5 1 576 2766 49 406 0.5 1 68 338 50 1842 0.5 1 348 1494 51 562 0.5 1 68 494 52 454 0.5 1 72 382 53 1812 0.5 1 304 1508 54 5032 0.5 1 1010 4022 55 2382 0.5 1 414 1968 56 1382 0.5 1 252 1130 57 2350 0.5 1 460 1890 58 1308 0.5 1 228 1080 59 742 0.5 1 116 626 60 1388 0.5 1 248 1140 61 2138 0.5 1 288 1850 62 4070 0.5 1 768 3302 63 1074 0.5 1 206 868 64 124 0.5 1 16 108 65 130 0.5 1 10 120 66 578 0.5 1 80 498 67 644 0.5 1 80 564 68 1936 0.5 1 306 1630 69 1826 0.5 1 290 1536 70 3286 0.5 1 582 2704 71 1290 0.5 1 204 1086 72 558 0.5 1 100 458 73 550 0.5 1 138 412 74 592 0.5 1 130 462 75 690 0.5 1 138 552 76 740 0.5 1 110 630 77 852 0.5 1 140 712 78 894 0.5 1 164 730 79 822 0.5 1 154 668 80 1464 0.5 1 318 1146 81 1060 0.5 1 226 834 82 1112 0.5 1 208 904 83 1020 0.5 1 210 810 84 796 0.5 1 158 638 85 1026 0.5 1 234 792 86 928 0.5 1 214 714 87 634 0.5 1 142 492 88 532 0.5 1 116 416 89 570 0.5 1 112 458 90 468 0.5 1 88 380 91 490 0.5 1 104 386 92 562 0.5 1 126 436 93 2122 0.5 1 462 1660 94 4226 0.5 1 868 3358 95 1006 0.5 1 208 798 96 502 0.5 1 116 386 97 4378 0.5 1 1096 3282 98 382 0.5 1 84 298 99 204 0.5 1 30 174 100 282 0.5 1 72 210 101 228 0.5 1 46 182 102 450 0.5 1 104 346 103 136 0.5 1 30 106 104 84 0.5 1 10 74 105 112 0.5 1 28 84 106 86 0.5 1 22 64 107 44 0.5 1 8 36 108 22 0.5 1 4 18 109 26 0.5 1 6 20 110 140 0.5 1 48 92 111 8 0.5 1 0 8 112 4 0.5 1 4 116 18 0.5 1 2 16 123 2 0.5 1 2 125 2 0.5 1 0 2 131 6 0.5 1 4 2 132 2 0.5 1 0 2 133 14 0.5 1 6 8 134 18 0.5 1 12 6 135 6 0.5 1 2 4 136 28 0.5 1 24 4 137 4934 0.5 1 4812 122 138 27080 0.5 1 25682 1398 139 2 0.5 1 2 140 4 0.5 1 0 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041595_val_1.fq.gz ============================================= 30665748 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1343238 (4.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13000518 (42.4%)