SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041684_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/raw_data/cup/BS_workflow/20201115/tmp/4556e7ae-3e8e-11eb-aa66-b4055d0383c6/trimmed/RRBS20A041684_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 478.23 s (23 us/read; 2.58 M reads/minute). === Summary === Total reads processed: 20,534,529 Reads with adapters: 8,504,657 (41.4%) Reads written (passing filters): 20,534,529 (100.0%) Total basepairs processed: 2,081,964,772 bp Total written (filtered): 2,050,181,880 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8504657 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 0.7% G: 22.7% T: 47.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6069465 5133632.2 0 6069465 2 1690125 1283408.1 0 1690125 3 414254 320852.0 0 414254 4 94629 80213.0 0 94629 5 4837 20053.3 0 4837 6 2619 5013.3 0 2619 7 2166 1253.3 0 2166 8 1662 313.3 0 1662 9 2968 78.3 0 2720 248 10 2314 19.6 1 934 1380 11 2379 4.9 1 475 1904 12 924 1.2 1 159 765 13 991 0.3 1 200 791 14 1877 0.3 1 370 1507 15 1601 0.3 1 317 1284 16 3761 0.3 1 682 3079 17 4858 0.3 1 1019 3839 18 1939 0.3 1 535 1404 19 116 0.3 1 15 101 20 954 0.3 1 172 782 21 102 0.3 1 18 84 22 159 0.3 1 27 132 23 819 0.3 1 138 681 24 3172 0.3 1 696 2476 25 1372 0.3 1 273 1099 26 337 0.3 1 68 269 27 1282 0.3 1 232 1050 28 2796 0.3 1 533 2263 29 2673 0.3 1 486 2187 30 521 0.3 1 94 427 31 91 0.3 1 10 81 32 1080 0.3 1 219 861 33 1663 0.3 1 274 1389 34 1753 0.3 1 358 1395 35 3309 0.3 1 701 2608 36 1358 0.3 1 283 1075 37 490 0.3 1 84 406 38 2079 0.3 1 398 1681 39 903 0.3 1 154 749 40 3066 0.3 1 618 2448 41 2059 0.3 1 398 1661 42 2244 0.3 1 479 1765 43 3454 0.3 1 738 2716 44 548 0.3 1 108 440 45 1675 0.3 1 328 1347 46 540 0.3 1 102 438 47 947 0.3 1 165 782 48 3408 0.3 1 723 2685 49 314 0.3 1 66 248 50 1150 0.3 1 224 926 51 432 0.3 1 93 339 52 304 0.3 1 60 244 53 751 0.3 1 132 619 54 2489 0.3 1 515 1974 55 1718 0.3 1 349 1369 56 829 0.3 1 175 654 57 1115 0.3 1 235 880 58 593 0.3 1 120 473 59 313 0.3 1 55 258 60 613 0.3 1 127 486 61 715 0.3 1 126 589 62 2595 0.3 1 605 1990 63 540 0.3 1 127 413 64 82 0.3 1 13 69 65 58 0.3 1 9 49 66 376 0.3 1 69 307 67 263 0.3 1 38 225 68 1346 0.3 1 287 1059 69 1355 0.3 1 276 1079 70 2475 0.3 1 537 1938 71 801 0.3 1 162 639 72 278 0.3 1 37 241 73 560 0.3 1 118 442 74 527 0.3 1 117 410 75 708 0.3 1 158 550 76 758 0.3 1 200 558 77 958 0.3 1 229 729 78 882 0.3 1 195 687 79 738 0.3 1 199 539 80 1140 0.3 1 208 932 81 869 0.3 1 198 671 82 921 0.3 1 195 726 83 979 0.3 1 274 705 84 766 0.3 1 172 594 85 1111 0.3 1 298 813 86 780 0.3 1 182 598 87 617 0.3 1 131 486 88 457 0.3 1 92 365 89 599 0.3 1 142 457 90 522 0.3 1 131 391 91 512 0.3 1 133 379 92 418 0.3 1 79 339 93 1121 0.3 1 263 858 94 2145 0.3 1 423 1722 95 675 0.3 1 168 507 96 415 0.3 1 104 311 97 1980 0.3 1 487 1493 98 334 0.3 1 93 241 99 225 0.3 1 62 163 100 263 0.3 1 60 203 101 263 0.3 1 60 203 102 376 0.3 1 100 276 103 174 0.3 1 53 121 104 134 0.3 1 38 96 105 98 0.3 1 19 79 106 82 0.3 1 21 61 107 56 0.3 1 15 41 108 32 0.3 1 11 21 109 25 0.3 1 0 25 110 103 0.3 1 15 88 111 6 0.3 1 3 3 112 2 0.3 1 1 1 113 3 0.3 1 2 1 114 5 0.3 1 1 4 115 6 0.3 1 1 5 116 10 0.3 1 1 9 120 1 0.3 1 0 1 122 1 0.3 1 0 1 124 2 0.3 1 2 125 3 0.3 1 3 127 2 0.3 1 0 2 128 1 0.3 1 1 129 6 0.3 1 5 1 130 4 0.3 1 2 2 131 12 0.3 1 10 2 132 12 0.3 1 7 5 133 39 0.3 1 19 20 134 58 0.3 1 44 14 135 52 0.3 1 44 8 136 142 0.3 1 126 16 137 11755 0.3 1 11352 403 138 99365 0.3 1 95723 3642 139 1 0.3 1 1 140 2 0.3 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041684_val_1.fq.gz ============================================= 20534529 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 776180 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 8504657 (41.4%)