SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041521_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/20201120/tmp/a6fb391a-5572-11eb-a954-6c92bfc12788/trimmed/RRBS20A041521_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 453.82 s (22 us/read; 2.76 M reads/minute). === Summary === Total reads processed: 20,854,664 Reads with adapters: 8,735,803 (41.9%) Reads written (passing filters): 20,854,664 (100.0%) Total basepairs processed: 2,125,482,466 bp Total written (filtered): 2,067,819,288 bp (97.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8735803 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 0.7% G: 22.3% T: 47.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6145124 5213666.0 0 6145124 2 1707706 1303416.5 0 1707706 3 383676 325854.1 0 383676 4 89176 81463.5 0 89176 5 4715 20365.9 0 4715 6 2373 5091.5 0 2373 7 1569 1272.9 0 1569 8 1411 318.2 0 1411 9 2263 79.6 0 2018 245 10 2492 19.9 1 901 1591 11 2239 5.0 1 290 1949 12 817 1.2 1 140 677 13 811 0.3 1 99 712 14 1637 0.3 1 203 1434 15 1032 0.3 1 128 904 16 3315 0.3 1 430 2885 17 4163 0.3 1 992 3171 18 3632 0.3 1 2093 1539 19 106 0.3 1 16 90 20 825 0.3 1 150 675 21 104 0.3 1 19 85 22 179 0.3 1 21 158 23 692 0.3 1 93 599 24 2580 0.3 1 453 2127 25 1019 0.3 1 158 861 26 510 0.3 1 66 444 27 1012 0.3 1 120 892 28 2156 0.3 1 317 1839 29 2339 0.3 1 300 2039 30 528 0.3 1 80 448 31 174 0.3 1 18 156 32 1050 0.3 1 142 908 33 1734 0.3 1 226 1508 34 1836 0.3 1 274 1562 35 1090 0.3 1 141 949 36 965 0.3 1 146 819 37 1658 0.3 1 265 1393 38 498 0.3 1 93 405 39 264 0.3 1 40 224 40 1346 0.3 1 153 1193 41 1045 0.3 1 122 923 42 1496 0.3 1 219 1277 43 2574 0.3 1 353 2221 44 512 0.3 1 56 456 45 1161 0.3 1 141 1020 46 365 0.3 1 33 332 47 758 0.3 1 94 664 48 1999 0.3 1 273 1726 49 139 0.3 1 18 121 50 1305 0.3 1 177 1128 51 349 0.3 1 35 314 52 207 0.3 1 21 186 53 828 0.3 1 100 728 54 3054 0.3 1 415 2639 55 1319 0.3 1 185 1134 56 760 0.3 1 98 662 57 1309 0.3 1 209 1100 58 749 0.3 1 72 677 59 366 0.3 1 55 311 60 640 0.3 1 94 546 61 874 0.3 1 95 779 62 2049 0.3 1 272 1777 63 724 0.3 1 98 626 64 81 0.3 1 8 73 65 52 0.3 1 4 48 66 161 0.3 1 22 139 67 262 0.3 1 31 231 68 1152 0.3 1 153 999 69 1144 0.3 1 177 967 70 2418 0.3 1 321 2097 71 1173 0.3 1 165 1008 72 449 0.3 1 40 409 73 325 0.3 1 37 288 74 423 0.3 1 55 368 75 542 0.3 1 83 459 76 642 0.3 1 108 534 77 649 0.3 1 87 562 78 516 0.3 1 70 446 79 585 0.3 1 92 493 80 622 0.3 1 80 542 81 550 0.3 1 87 463 82 715 0.3 1 98 617 83 737 0.3 1 110 627 84 526 0.3 1 76 450 85 645 0.3 1 87 558 86 647 0.3 1 80 567 87 393 0.3 1 45 348 88 358 0.3 1 43 315 89 440 0.3 1 58 382 90 334 0.3 1 43 291 91 302 0.3 1 41 261 92 288 0.3 1 36 252 93 1345 0.3 1 153 1192 94 1865 0.3 1 182 1683 95 463 0.3 1 56 407 96 266 0.3 1 44 222 97 1244 0.3 1 123 1121 98 256 0.3 1 40 216 99 170 0.3 1 24 146 100 171 0.3 1 19 152 101 161 0.3 1 18 143 102 360 0.3 1 65 295 103 123 0.3 1 14 109 104 73 0.3 1 6 67 105 56 0.3 1 9 47 106 51 0.3 1 8 43 107 27 0.3 1 3 24 108 18 0.3 1 1 17 109 17 0.3 1 1 16 110 27 0.3 1 2 25 111 5 0.3 1 0 5 112 3 0.3 1 2 1 113 1 0.3 1 0 1 114 2 0.3 1 2 116 1 0.3 1 1 117 3 0.3 1 3 119 1 0.3 1 0 1 120 3 0.3 1 1 2 121 3 0.3 1 3 122 2 0.3 1 0 2 123 2 0.3 1 2 124 2 0.3 1 2 125 1 0.3 1 1 126 5 0.3 1 4 1 127 5 0.3 1 3 2 128 4 0.3 1 3 1 129 8 0.3 1 8 130 8 0.3 1 7 1 131 15 0.3 1 10 5 132 19 0.3 1 15 4 133 43 0.3 1 29 14 134 59 0.3 1 52 7 135 81 0.3 1 70 11 136 153 0.3 1 130 23 137 6885 0.3 1 6674 211 138 299261 0.3 1 293595 5666 140 6 0.3 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041521_val_1.fq.gz ============================================= 20854664 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 728611 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 8735800 (41.9%)