SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041611_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/5e97a914-48bc-11eb-919a-6c92bfc12ed8/trimmed/RRBS20A041611_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 372.59 s (23 us/read; 2.66 M reads/minute). === Summary === Total reads processed: 16,498,696 Reads with adapters: 6,701,549 (40.6%) Reads written (passing filters): 16,498,696 (100.0%) Total basepairs processed: 1,594,850,661 bp Total written (filtered): 1,577,732,535 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6701549 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 0.7% G: 20.4% T: 48.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4960551 4124674.0 0 4960551 2 1249038 1031168.5 0 1249038 3 308488 257792.1 0 308488 4 69678 64448.0 0 69678 5 3655 16112.0 0 3655 6 1678 4028.0 0 1678 7 1333 1007.0 0 1333 8 790 251.8 0 790 9 1082 62.9 0 892 190 10 1957 15.7 1 445 1512 11 1180 3.9 1 105 1075 12 559 1.0 1 68 491 13 579 0.2 1 65 514 14 1011 0.2 1 86 925 15 805 0.2 1 74 731 16 1961 0.2 1 158 1803 17 3086 0.2 1 273 2813 18 1195 0.2 1 207 988 19 59 0.2 1 8 51 20 610 0.2 1 59 551 21 61 0.2 1 7 54 22 75 0.2 1 8 67 23 646 0.2 1 69 577 24 1456 0.2 1 170 1286 25 781 0.2 1 90 691 26 232 0.2 1 18 214 27 852 0.2 1 74 778 28 1423 0.2 1 139 1284 29 1312 0.2 1 112 1200 30 447 0.2 1 52 395 31 57 0.2 1 3 54 32 676 0.2 1 77 599 33 1356 0.2 1 117 1239 34 1507 0.2 1 164 1343 35 358 0.2 1 38 320 36 867 0.2 1 80 787 37 129 0.2 1 10 119 38 1559 0.2 1 141 1418 39 1228 0.2 1 105 1123 40 464 0.2 1 50 414 41 1529 0.2 1 144 1385 42 154 0.2 1 8 146 43 1816 0.2 1 185 1631 44 329 0.2 1 28 301 45 890 0.2 1 91 799 46 342 0.2 1 30 312 47 767 0.2 1 64 703 48 1593 0.2 1 158 1435 49 178 0.2 1 19 159 50 908 0.2 1 81 827 51 287 0.2 1 25 262 52 238 0.2 1 19 219 53 824 0.2 1 69 755 54 1807 0.2 1 169 1638 55 1190 0.2 1 121 1069 56 635 0.2 1 56 579 57 1152 0.2 1 122 1030 58 766 0.2 1 96 670 59 365 0.2 1 34 331 60 891 0.2 1 69 822 61 1120 0.2 1 116 1004 62 2710 0.2 1 355 2355 63 664 0.2 1 85 579 64 120 0.2 1 13 107 65 137 0.2 1 13 124 66 469 0.2 1 55 414 67 335 0.2 1 26 309 68 874 0.2 1 81 793 69 1010 0.2 1 94 916 70 1886 0.2 1 172 1714 71 849 0.2 1 64 785 72 446 0.2 1 31 415 73 469 0.2 1 46 423 74 347 0.2 1 31 316 75 373 0.2 1 34 339 76 387 0.2 1 35 352 77 471 0.2 1 39 432 78 424 0.2 1 41 383 79 432 0.2 1 47 385 80 601 0.2 1 55 546 81 426 0.2 1 31 395 82 505 0.2 1 33 472 83 509 0.2 1 43 466 84 464 0.2 1 48 416 85 634 0.2 1 51 583 86 470 0.2 1 45 425 87 305 0.2 1 17 288 88 302 0.2 1 26 276 89 382 0.2 1 40 342 90 331 0.2 1 21 310 91 328 0.2 1 24 304 92 281 0.2 1 27 254 93 634 0.2 1 57 577 94 826 0.2 1 65 761 95 294 0.2 1 16 278 96 288 0.2 1 22 266 97 725 0.2 1 54 671 98 211 0.2 1 21 190 99 150 0.2 1 13 137 100 144 0.2 1 11 133 101 153 0.2 1 9 144 102 266 0.2 1 38 228 103 129 0.2 1 16 113 104 95 0.2 1 10 85 105 70 0.2 1 6 64 106 67 0.2 1 6 61 107 45 0.2 1 7 38 108 20 0.2 1 2 18 109 26 0.2 1 3 23 110 52 0.2 1 6 46 111 11 0.2 1 2 9 112 5 0.2 1 0 5 113 1 0.2 1 0 1 114 2 0.2 1 1 1 124 2 0.2 1 2 125 1 0.2 1 1 126 2 0.2 1 1 1 128 4 0.2 1 2 2 129 5 0.2 1 4 1 130 2 0.2 1 1 1 131 3 0.2 1 2 1 132 5 0.2 1 5 133 36 0.2 1 14 22 134 37 0.2 1 30 7 135 15 0.2 1 11 4 136 56 0.2 1 47 9 137 1772 0.2 1 1682 90 138 34892 0.2 1 33830 1062 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041611_val_1.fq.gz ============================================= 16498696 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 865901 (5.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6701549 (40.6%)