SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041598_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/5f253f18-48bc-11eb-991a-b4055d0383c6/trimmed/RRBS20A041598_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 12023.57 s (269 us/read; 0.22 M reads/minute). === Summary === Total reads processed: 44,705,946 Reads with adapters: 13,739,652 (30.7%) Reads written (passing filters): 44,705,946 (100.0%) Total basepairs processed: 4,499,658,494 bp Total written (filtered): 4,468,489,740 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13739652 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.3% C: 73.5% G: 0.7% T: 6.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13435506 11176486.5 0 13435506 2 105026 2794121.6 0 105026 3 10580 698530.4 0 10580 4 14364 174632.6 0 14364 5 4338 43658.2 0 4338 6 1470 10914.5 0 1470 7 2286 2728.6 0 2286 8 2152 682.2 0 2152 9 658 170.5 0 634 24 10 4312 42.6 1 570 3742 11 188 10.7 1 24 164 12 714 2.7 1 64 650 13 898 0.7 1 58 840 14 1046 0.7 1 44 1002 15 592 0.7 1 22 570 16 772 0.7 1 42 730 17 900 0.7 1 46 854 18 476 0.7 1 22 454 19 1056 0.7 1 48 1008 20 1040 0.7 1 58 982 21 56 0.7 1 4 52 22 196 0.7 1 12 184 23 878 0.7 1 54 824 24 2198 0.7 1 96 2102 25 942 0.7 1 58 884 26 1544 0.7 1 96 1448 27 314 0.7 1 18 296 28 458 0.7 1 24 434 29 156 0.7 1 10 146 30 356 0.7 1 16 340 31 684 0.7 1 48 636 32 982 0.7 1 56 926 33 1992 0.7 1 116 1876 34 214 0.7 1 18 196 35 344 0.7 1 24 320 36 262 0.7 1 6 256 37 780 0.7 1 38 742 38 420 0.7 1 18 402 39 498 0.7 1 30 468 40 578 0.7 1 40 538 41 532 0.7 1 38 494 42 632 0.7 1 40 592 43 424 0.7 1 18 406 44 580 0.7 1 34 546 45 1144 0.7 1 48 1096 46 690 0.7 1 28 662 47 460 0.7 1 14 446 48 820 0.7 1 48 772 49 806 0.7 1 50 756 50 694 0.7 1 42 652 51 826 0.7 1 34 792 52 982 0.7 1 60 922 53 366 0.7 1 22 344 54 626 0.7 1 28 598 55 604 0.7 1 24 580 56 190 0.7 1 0 190 57 618 0.7 1 20 598 58 750 0.7 1 30 720 59 490 0.7 1 36 454 60 572 0.7 1 40 532 61 674 0.7 1 48 626 62 924 0.7 1 60 864 63 952 0.7 1 70 882 64 456 0.7 1 40 416 65 378 0.7 1 26 352 66 1120 0.7 1 54 1066 67 538 0.7 1 38 500 68 472 0.7 1 20 452 69 434 0.7 1 20 414 70 422 0.7 1 18 404 71 452 0.7 1 24 428 72 376 0.7 1 14 362 73 412 0.7 1 20 392 74 376 0.7 1 24 352 75 898 0.7 1 58 840 76 588 0.7 1 42 546 77 520 0.7 1 22 498 78 380 0.7 1 16 364 79 424 0.7 1 22 402 80 382 0.7 1 12 370 81 364 0.7 1 14 350 82 464 0.7 1 22 442 83 446 0.7 1 24 422 84 504 0.7 1 36 468 85 522 0.7 1 30 492 86 302 0.7 1 26 276 87 248 0.7 1 8 240 88 226 0.7 1 8 218 89 218 0.7 1 12 206 90 184 0.7 1 2 182 91 158 0.7 1 6 152 92 206 0.7 1 22 184 93 194 0.7 1 10 184 94 244 0.7 1 12 232 95 144 0.7 1 10 134 96 136 0.7 1 12 124 97 178 0.7 1 6 172 98 140 0.7 1 8 132 99 206 0.7 1 10 196 100 164 0.7 1 8 156 101 108 0.7 1 2 106 102 224 0.7 1 22 202 103 84 0.7 1 4 80 104 40 0.7 1 6 34 105 74 0.7 1 2 72 106 32 0.7 1 0 32 107 22 0.7 1 4 18 108 18 0.7 1 0 18 109 22 0.7 1 4 18 110 22 0.7 1 0 22 111 12 0.7 1 0 12 112 2 0.7 1 0 2 115 2 0.7 1 0 2 116 8 0.7 1 8 117 2 0.7 1 2 118 2 0.7 1 0 2 121 2 0.7 1 2 122 2 0.7 1 2 123 2 0.7 1 2 124 2 0.7 1 2 125 4 0.7 1 4 127 6 0.7 1 6 128 8 0.7 1 8 129 8 0.7 1 8 130 6 0.7 1 4 2 131 4 0.7 1 4 132 12 0.7 1 12 133 12 0.7 1 12 134 26 0.7 1 24 2 135 46 0.7 1 44 2 136 102 0.7 1 96 6 137 4244 0.7 1 4146 98 138 103034 0.7 1 101398 1636 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041598_val_2.fq.gz ============================================= 44705946 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2279556 (5.1%) 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: 44705946 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 212950 (0.48%)