SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041595_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/599cb8d2-48bc-11eb-9653-6c92bfbea1ec/trimmed/RRBS20A041595_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 710.39 s (23 us/read; 2.59 M reads/minute). === Summary === Total reads processed: 30,665,748 Reads with adapters: 11,581,916 (37.8%) Reads written (passing filters): 30,665,748 (100.0%) Total basepairs processed: 3,040,575,274 bp Total written (filtered): 3,021,633,646 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11581916 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.9% C: 74.4% G: 1.7% T: 6.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11325600 7666437.0 0 11325600 2 110734 1916609.2 0 110734 3 25270 479152.3 0 25270 4 12000 119788.1 0 12000 5 3754 29947.0 0 3754 6 1366 7486.8 0 1366 7 2098 1871.7 0 2098 8 1002 467.9 0 1002 9 688 117.0 0 652 36 10 5918 29.2 1 1310 4608 11 220 7.3 1 18 202 12 4348 1.8 1 914 3434 13 1024 0.5 1 100 924 14 1420 0.5 1 116 1304 15 432 0.5 1 40 392 16 594 0.5 1 46 548 17 1124 0.5 1 86 1038 18 546 0.5 1 40 506 19 1322 0.5 1 124 1198 20 1106 0.5 1 86 1020 21 66 0.5 1 4 62 22 754 0.5 1 82 672 23 922 0.5 1 74 848 24 2824 0.5 1 226 2598 25 952 0.5 1 74 878 26 1166 0.5 1 114 1052 27 500 0.5 1 62 438 28 1216 0.5 1 98 1118 29 130 0.5 1 10 120 30 1062 0.5 1 96 966 31 748 0.5 1 80 668 32 1168 0.5 1 90 1078 33 1834 0.5 1 204 1630 34 624 0.5 1 50 574 35 942 0.5 1 88 854 36 352 0.5 1 22 330 37 990 0.5 1 94 896 38 518 0.5 1 52 466 39 538 0.5 1 64 474 40 490 0.5 1 54 436 41 644 0.5 1 28 616 42 786 0.5 1 54 732 43 550 0.5 1 52 498 44 626 0.5 1 52 574 45 1064 0.5 1 110 954 46 734 0.5 1 56 678 47 448 0.5 1 36 412 48 948 0.5 1 72 876 49 714 0.5 1 82 632 50 766 0.5 1 90 676 51 970 0.5 1 92 878 52 930 0.5 1 88 842 53 522 0.5 1 54 468 54 762 0.5 1 76 686 55 714 0.5 1 80 634 56 266 0.5 1 24 242 57 570 0.5 1 42 528 58 868 0.5 1 90 778 59 552 0.5 1 58 494 60 650 0.5 1 60 590 61 778 0.5 1 48 730 62 1054 0.5 1 106 948 63 968 0.5 1 106 862 64 502 0.5 1 46 456 65 482 0.5 1 56 426 66 930 0.5 1 86 844 67 598 0.5 1 68 530 68 550 0.5 1 60 490 69 494 0.5 1 46 448 70 436 0.5 1 30 406 71 442 0.5 1 38 404 72 442 0.5 1 28 414 73 442 0.5 1 48 394 74 410 0.5 1 52 358 75 672 0.5 1 78 594 76 840 0.5 1 88 752 77 612 0.5 1 56 556 78 438 0.5 1 26 412 79 476 0.5 1 24 452 80 380 0.5 1 38 342 81 412 0.5 1 24 388 82 450 0.5 1 32 418 83 418 0.5 1 34 384 84 436 0.5 1 54 382 85 468 0.5 1 40 428 86 280 0.5 1 24 256 87 300 0.5 1 26 274 88 264 0.5 1 32 232 89 230 0.5 1 32 198 90 206 0.5 1 12 194 91 150 0.5 1 16 134 92 158 0.5 1 14 144 93 178 0.5 1 16 162 94 228 0.5 1 12 216 95 160 0.5 1 16 144 96 154 0.5 1 20 134 97 126 0.5 1 10 116 98 96 0.5 1 4 92 99 118 0.5 1 22 96 100 114 0.5 1 6 108 101 86 0.5 1 2 84 102 112 0.5 1 10 102 103 70 0.5 1 6 64 104 50 0.5 1 2 48 105 26 0.5 1 4 22 106 16 0.5 1 2 14 107 26 0.5 1 2 24 108 18 0.5 1 2 16 109 24 0.5 1 2 22 110 22 0.5 1 4 18 111 10 0.5 1 0 10 112 2 0.5 1 0 2 115 2 0.5 1 2 116 6 0.5 1 2 4 126 2 0.5 1 2 129 2 0.5 1 2 130 2 0.5 1 2 131 2 0.5 1 2 132 4 0.5 1 4 133 2 0.5 1 0 2 134 4 0.5 1 4 135 6 0.5 1 6 136 54 0.5 1 50 4 137 4968 0.5 1 4864 104 138 27060 0.5 1 26570 490 139 2 0.5 1 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041595_val_2.fq.gz ============================================= 30665748 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1704674 (5.6%) 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: 30665748 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 100226 (0.33%)