SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041523_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/5e10db8c-48bc-11eb-8417-6c92bfc12ef6/trimmed/RRBS20A041523_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1162.55 s (24 us/read; 2.50 M reads/minute). === Summary === Total reads processed: 48,410,430 Reads with adapters: 19,059,436 (39.4%) Reads written (passing filters): 48,410,430 (100.0%) Total basepairs processed: 5,008,247,694 bp Total written (filtered): 4,960,547,100 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19059436 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.2% C: 60.7% G: 2.4% T: 9.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18453084 12102607.5 0 18453084 2 281674 3025651.9 0 281674 3 34128 756413.0 0 34128 4 16000 189103.2 0 16000 5 5182 47275.8 0 5182 6 2398 11819.0 0 2398 7 3964 2954.7 0 3964 8 1678 738.7 0 1678 9 872 184.7 0 744 128 10 9958 46.2 1 1974 7984 11 372 11.5 1 38 334 12 7264 2.9 1 1314 5950 13 1382 0.7 1 136 1246 14 1784 0.7 1 96 1688 15 760 0.7 1 24 736 16 804 0.7 1 58 746 17 1314 0.7 1 76 1238 18 610 0.7 1 32 578 19 1322 0.7 1 84 1238 20 1186 0.7 1 54 1132 21 84 0.7 1 4 80 22 864 0.7 1 44 820 23 1082 0.7 1 54 1028 24 2850 0.7 1 138 2712 25 864 0.7 1 52 812 26 1018 0.7 1 46 972 27 372 0.7 1 8 364 28 1142 0.7 1 74 1068 29 156 0.7 1 10 146 30 1054 0.7 1 60 994 31 814 0.7 1 36 778 32 1160 0.7 1 66 1094 33 1846 0.7 1 114 1732 34 524 0.7 1 22 502 35 1048 0.7 1 76 972 36 306 0.7 1 8 298 37 934 0.7 1 46 888 38 432 0.7 1 36 396 39 534 0.7 1 36 498 40 470 0.7 1 32 438 41 682 0.7 1 40 642 42 788 0.7 1 64 724 43 396 0.7 1 18 378 44 572 0.7 1 32 540 45 1156 0.7 1 78 1078 46 602 0.7 1 32 570 47 418 0.7 1 18 400 48 1024 0.7 1 84 940 49 568 0.7 1 46 522 50 624 0.7 1 50 574 51 970 0.7 1 78 892 52 1088 0.7 1 78 1010 53 462 0.7 1 20 442 54 692 0.7 1 62 630 55 706 0.7 1 56 650 56 308 0.7 1 18 290 57 756 0.7 1 56 700 58 904 0.7 1 48 856 59 522 0.7 1 48 474 60 616 0.7 1 46 570 61 754 0.7 1 72 682 62 848 0.7 1 116 732 63 820 0.7 1 78 742 64 454 0.7 1 22 432 65 466 0.7 1 40 426 66 1072 0.7 1 114 958 67 596 0.7 1 42 554 68 506 0.7 1 42 464 69 472 0.7 1 36 436 70 424 0.7 1 22 402 71 482 0.7 1 38 444 72 438 0.7 1 34 404 73 382 0.7 1 32 350 74 342 0.7 1 36 306 75 776 0.7 1 52 724 76 830 0.7 1 50 780 77 758 0.7 1 58 700 78 364 0.7 1 16 348 79 422 0.7 1 24 398 80 388 0.7 1 38 350 81 380 0.7 1 22 358 82 336 0.7 1 20 316 83 420 0.7 1 28 392 84 412 0.7 1 24 388 85 394 0.7 1 34 360 86 304 0.7 1 20 284 87 238 0.7 1 10 228 88 176 0.7 1 8 168 89 190 0.7 1 16 174 90 198 0.7 1 18 180 91 162 0.7 1 10 152 92 186 0.7 1 16 170 93 196 0.7 1 18 178 94 192 0.7 1 14 178 95 112 0.7 1 4 108 96 128 0.7 1 6 122 97 152 0.7 1 10 142 98 120 0.7 1 10 110 99 146 0.7 1 10 136 100 124 0.7 1 12 112 101 82 0.7 1 4 78 102 150 0.7 1 14 136 103 66 0.7 1 6 60 104 34 0.7 1 4 30 105 42 0.7 1 10 32 106 42 0.7 1 0 42 107 32 0.7 1 6 26 108 30 0.7 1 4 26 109 26 0.7 1 6 20 110 26 0.7 1 2 24 111 6 0.7 1 2 4 113 2 0.7 1 0 2 115 6 0.7 1 6 116 4 0.7 1 4 117 2 0.7 1 2 118 2 0.7 1 0 2 119 2 0.7 1 2 120 2 0.7 1 0 2 123 2 0.7 1 2 124 2 0.7 1 2 125 4 0.7 1 2 2 126 8 0.7 1 8 127 6 0.7 1 6 128 14 0.7 1 12 2 129 24 0.7 1 22 2 130 26 0.7 1 22 4 131 34 0.7 1 30 4 132 24 0.7 1 22 2 133 36 0.7 1 32 4 134 54 0.7 1 48 6 135 118 0.7 1 102 16 136 292 0.7 1 262 30 137 5596 0.7 1 5384 212 138 179336 0.7 1 175322 4014 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041523_val_2.fq.gz ============================================= 48410430 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2440026 (5.0%) 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: 48410430 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 281314 (0.58%)