SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041522_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/20201110/tmp/cbb16130-5581-11eb-b8bb-6c92bfc1303a/trimmed/RRBS20A041522_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 276.48 s (23 us/read; 2.66 M reads/minute). === Summary === Total reads processed: 12,262,650 Reads with adapters: 4,975,716 (40.6%) Reads written (passing filters): 12,262,650 (100.0%) Total basepairs processed: 1,191,054,247 bp Total written (filtered): 1,160,481,389 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4975716 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 1.0% G: 24.4% T: 46.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3456604 3065662.5 0 3456604 2 977630 766415.6 0 977630 3 238497 191603.9 0 238497 4 55457 47901.0 0 55457 5 3955 11975.2 0 3955 6 2276 2993.8 0 2276 7 2009 748.5 0 2009 8 1646 187.1 0 1646 9 2415 46.8 0 2261 154 10 2009 11.7 1 1042 967 11 1538 2.9 1 332 1206 12 617 0.7 1 143 474 13 740 0.2 1 160 580 14 1599 0.2 1 325 1274 15 1120 0.2 1 225 895 16 3419 0.2 1 659 2760 17 3713 0.2 1 812 2901 18 1669 0.2 1 665 1004 19 72 0.2 1 14 58 20 660 0.2 1 129 531 21 74 0.2 1 21 53 22 190 0.2 1 27 163 23 697 0.2 1 147 550 24 2688 0.2 1 590 2098 25 1177 0.2 1 257 920 26 391 0.2 1 75 316 27 806 0.2 1 170 636 28 2120 0.2 1 452 1668 29 2231 0.2 1 423 1808 30 473 0.2 1 104 369 31 156 0.2 1 23 133 32 885 0.2 1 170 715 33 1727 0.2 1 356 1371 34 2328 0.2 1 541 1787 35 851 0.2 1 180 671 36 858 0.2 1 174 684 37 2156 0.2 1 527 1629 38 488 0.2 1 131 357 39 398 0.2 1 96 302 40 1686 0.2 1 366 1320 41 1314 0.2 1 289 1025 42 2045 0.2 1 504 1541 43 3317 0.2 1 704 2613 44 477 0.2 1 87 390 45 1306 0.2 1 293 1013 46 399 0.2 1 71 328 47 736 0.2 1 136 600 48 2536 0.2 1 554 1982 49 246 0.2 1 42 204 50 1027 0.2 1 192 835 51 395 0.2 1 73 322 52 277 0.2 1 60 217 53 637 0.2 1 133 504 54 1984 0.2 1 487 1497 55 1308 0.2 1 316 992 56 702 0.2 1 112 590 57 927 0.2 1 211 716 58 470 0.2 1 91 379 59 292 0.2 1 51 241 60 485 0.2 1 106 379 61 607 0.2 1 111 496 62 3132 0.2 1 774 2358 63 500 0.2 1 128 372 64 108 0.2 1 21 87 65 59 0.2 1 12 47 66 1072 0.2 1 257 815 67 227 0.2 1 39 188 68 1092 0.2 1 217 875 69 1188 0.2 1 224 964 70 1927 0.2 1 382 1545 71 427 0.2 1 69 358 72 140 0.2 1 32 108 73 489 0.2 1 112 377 74 457 0.2 1 81 376 75 662 0.2 1 153 509 76 754 0.2 1 177 577 77 903 0.2 1 220 683 78 845 0.2 1 205 640 79 833 0.2 1 192 641 80 997 0.2 1 222 775 81 917 0.2 1 214 703 82 904 0.2 1 222 682 83 946 0.2 1 180 766 84 777 0.2 1 181 596 85 995 0.2 1 218 777 86 732 0.2 1 161 571 87 668 0.2 1 153 515 88 523 0.2 1 112 411 89 717 0.2 1 190 527 90 569 0.2 1 121 448 91 672 0.2 1 166 506 92 486 0.2 1 105 381 93 1048 0.2 1 227 821 94 2027 0.2 1 436 1591 95 585 0.2 1 129 456 96 471 0.2 1 96 375 97 1773 0.2 1 408 1365 98 455 0.2 1 109 346 99 277 0.2 1 74 203 100 289 0.2 1 56 233 101 219 0.2 1 40 179 102 400 0.2 1 118 282 103 171 0.2 1 44 127 104 100 0.2 1 21 79 105 97 0.2 1 23 74 106 85 0.2 1 19 66 107 53 0.2 1 9 44 108 25 0.2 1 6 19 109 35 0.2 1 8 27 110 21 0.2 1 4 17 111 22 0.2 1 3 19 112 8 0.2 1 3 5 114 3 0.2 1 1 2 115 1 0.2 1 1 116 13 0.2 1 2 11 119 1 0.2 1 1 120 3 0.2 1 2 1 121 1 0.2 1 1 122 4 0.2 1 4 124 1 0.2 1 1 125 2 0.2 1 2 126 2 0.2 1 1 1 127 3 0.2 1 1 2 128 5 0.2 1 3 2 129 8 0.2 1 5 3 130 6 0.2 1 3 3 131 7 0.2 1 5 2 132 22 0.2 1 19 3 133 45 0.2 1 31 14 134 52 0.2 1 46 6 135 63 0.2 1 51 12 136 211 0.2 1 173 38 137 28499 0.2 1 27848 651 138 112367 0.2 1 109400 2967 140 6 0.2 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041522_val_1.fq.gz ============================================= 12262650 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 520999 (4.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 4975714 (40.6%)