SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041523_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/5e10db8c-48bc-11eb-8417-6c92bfc12ef6/trimmed/RRBS20A041523_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1108.41 s (23 us/read; 2.62 M reads/minute). === Summary === Total reads processed: 48,410,430 Reads with adapters: 21,955,360 (45.4%) Reads written (passing filters): 48,410,430 (100.0%) Total basepairs processed: 5,086,890,348 bp Total written (filtered): 5,021,374,800 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21955360 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.1% C: 1.0% G: 19.6% T: 48.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15893418 12102607.5 0 15893418 2 4181904 3025651.9 0 4181904 3 1085750 756413.0 0 1085750 4 234066 189103.2 0 234066 5 36996 47275.8 0 36996 6 19786 11819.0 0 19786 7 17868 2954.7 0 17868 8 19620 738.7 0 19620 9 21756 184.7 0 20614 1142 10 23250 46.2 1 14742 8508 11 7928 11.5 1 1046 6882 12 3362 2.9 1 454 2908 13 3774 0.7 1 558 3216 14 5430 0.7 1 694 4736 15 4512 0.7 1 514 3998 16 9708 0.7 1 1342 8366 17 12426 0.7 1 2334 10092 18 7502 0.7 1 2690 4812 19 330 0.7 1 30 300 20 3364 0.7 1 572 2792 21 152 0.7 1 18 134 22 334 0.7 1 36 298 23 2876 0.7 1 378 2498 24 6276 0.7 1 848 5428 25 3538 0.7 1 630 2908 26 744 0.7 1 78 666 27 3484 0.7 1 476 3008 28 5970 0.7 1 862 5108 29 5790 0.7 1 762 5028 30 1794 0.7 1 278 1516 31 470 0.7 1 34 436 32 3954 0.7 1 598 3356 33 4188 0.7 1 564 3624 34 5128 0.7 1 694 4434 35 3206 0.7 1 420 2786 36 2728 0.7 1 376 2352 37 4324 0.7 1 646 3678 38 1004 0.7 1 192 812 39 402 0.7 1 52 350 40 3302 0.7 1 396 2906 41 2554 0.7 1 306 2248 42 3728 0.7 1 554 3174 43 6278 0.7 1 782 5496 44 1086 0.7 1 96 990 45 3426 0.7 1 530 2896 46 1050 0.7 1 128 922 47 2796 0.7 1 342 2454 48 4660 0.7 1 694 3966 49 686 0.7 1 68 618 50 3062 0.7 1 430 2632 51 848 0.7 1 112 736 52 740 0.7 1 84 656 53 2820 0.7 1 412 2408 54 6978 0.7 1 920 6058 55 3064 0.7 1 402 2662 56 2116 0.7 1 322 1794 57 3562 0.7 1 554 3008 58 2210 0.7 1 316 1894 59 1074 0.7 1 126 948 60 2206 0.7 1 288 1918 61 2920 0.7 1 446 2474 62 5024 0.7 1 732 4292 63 1668 0.7 1 210 1458 64 140 0.7 1 10 130 65 124 0.7 1 10 114 66 546 0.7 1 76 470 67 944 0.7 1 116 828 68 2658 0.7 1 448 2210 69 2958 0.7 1 366 2592 70 5494 0.7 1 704 4790 71 1984 0.7 1 278 1706 72 948 0.7 1 112 836 73 554 0.7 1 56 498 74 568 0.7 1 72 496 75 1002 0.7 1 124 878 76 1290 0.7 1 214 1076 77 1206 0.7 1 170 1036 78 1316 0.7 1 154 1162 79 1186 0.7 1 174 1012 80 1418 0.7 1 212 1206 81 1178 0.7 1 158 1020 82 1612 0.7 1 186 1426 83 1914 0.7 1 298 1616 84 1154 0.7 1 194 960 85 1194 0.7 1 142 1052 86 1326 0.7 1 158 1168 87 1008 0.7 1 148 860 88 844 0.7 1 124 720 89 780 0.7 1 114 666 90 734 0.7 1 96 638 91 634 0.7 1 82 552 92 684 0.7 1 90 594 93 2754 0.7 1 262 2492 94 4260 0.7 1 418 3842 95 1080 0.7 1 94 986 96 606 0.7 1 72 534 97 3052 0.7 1 368 2684 98 508 0.7 1 84 424 99 282 0.7 1 44 238 100 334 0.7 1 44 290 101 318 0.7 1 38 280 102 544 0.7 1 78 466 103 200 0.7 1 28 172 104 156 0.7 1 14 142 105 104 0.7 1 14 90 106 128 0.7 1 18 110 107 84 0.7 1 18 66 108 38 0.7 1 2 36 109 44 0.7 1 8 36 110 138 0.7 1 4 134 111 20 0.7 1 8 12 112 10 0.7 1 2 8 113 2 0.7 1 2 114 2 0.7 1 0 2 117 4 0.7 1 2 2 118 2 0.7 1 2 119 2 0.7 1 0 2 120 4 0.7 1 2 2 121 2 0.7 1 0 2 123 4 0.7 1 2 2 124 6 0.7 1 6 126 4 0.7 1 2 2 127 8 0.7 1 2 6 128 10 0.7 1 2 8 129 10 0.7 1 6 4 130 4 0.7 1 4 131 12 0.7 1 10 2 132 28 0.7 1 18 10 133 38 0.7 1 12 26 134 68 0.7 1 62 6 135 68 0.7 1 52 16 136 118 0.7 1 96 22 137 4490 0.7 1 4300 190 138 181422 0.7 1 177036 4386 140 24 0.7 1 0 24 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041523_val_1.fq.gz ============================================= 48410430 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1817954 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 21955352 (45.4%)