SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041628_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/20201110/tmp/c91a8e10-5581-11eb-8c95-6c92bfc39756/trimmed/RRBS20A041628_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1881.11 s (50 us/read; 1.21 M reads/minute). === Summary === Total reads processed: 37,837,628 Reads with adapters: 14,067,566 (37.2%) Reads written (passing filters): 37,837,628 (100.0%) Total basepairs processed: 3,715,586,085 bp Total written (filtered): 3,615,501,323 bp (97.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14067566 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.1% C: 68.6% G: 5.4% T: 6.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13256273 9459407.0 0 13256273 2 123990 2364851.8 0 123990 3 9264 591212.9 0 9264 4 6135 147803.2 0 6135 5 2013 36950.8 0 2013 6 1280 9237.7 0 1280 7 2456 2309.4 0 2456 8 1109 577.4 0 1109 9 494 144.3 0 452 42 10 4112 36.1 1 1116 2996 11 156 9.0 1 19 137 12 3420 2.3 1 734 2686 13 1044 0.6 1 144 900 14 1154 0.6 1 123 1031 15 388 0.6 1 25 363 16 436 0.6 1 49 387 17 1029 0.6 1 93 936 18 337 0.6 1 23 314 19 1162 0.6 1 105 1057 20 650 0.6 1 57 593 21 83 0.6 1 25 58 22 595 0.6 1 36 559 23 919 0.6 1 59 860 24 2733 0.6 1 206 2527 25 585 0.6 1 40 545 26 1138 0.6 1 88 1050 27 346 0.6 1 24 322 28 636 0.6 1 57 579 29 56 0.6 1 4 52 30 627 0.6 1 45 582 31 662 0.6 1 45 617 32 727 0.6 1 60 667 33 1844 0.6 1 143 1701 34 469 0.6 1 33 436 35 612 0.6 1 64 548 36 101 0.6 1 10 91 37 807 0.6 1 74 733 38 211 0.6 1 21 190 39 246 0.6 1 20 226 40 247 0.6 1 27 220 41 564 0.6 1 36 528 42 958 0.6 1 54 904 43 290 0.6 1 23 267 44 495 0.6 1 47 448 45 1480 0.6 1 105 1375 46 496 0.6 1 32 464 47 211 0.6 1 17 194 48 954 0.6 1 80 874 49 319 0.6 1 32 287 50 672 0.6 1 47 625 51 930 0.6 1 81 849 52 855 0.6 1 77 778 53 96 0.6 1 7 89 54 413 0.6 1 31 382 55 316 0.6 1 27 289 56 41 0.6 1 5 36 57 264 0.6 1 19 245 58 698 0.6 1 45 653 59 342 0.6 1 31 311 60 620 0.6 1 95 525 61 815 0.6 1 163 652 62 1031 0.6 1 266 765 63 811 0.6 1 189 622 64 311 0.6 1 54 257 65 280 0.6 1 35 245 66 757 0.6 1 86 671 67 534 0.6 1 63 471 68 473 0.6 1 37 436 69 384 0.6 1 36 348 70 418 0.6 1 36 382 71 388 0.6 1 41 347 72 343 0.6 1 29 314 73 366 0.6 1 42 324 74 387 0.6 1 35 352 75 477 0.6 1 39 438 76 615 0.6 1 56 559 77 543 0.6 1 45 498 78 357 0.6 1 26 331 79 388 0.6 1 31 357 80 427 0.6 1 48 379 81 377 0.6 1 25 352 82 408 0.6 1 35 373 83 519 0.6 1 45 474 84 551 0.6 1 61 490 85 453 0.6 1 45 408 86 312 0.6 1 20 292 87 258 0.6 1 13 245 88 294 0.6 1 22 272 89 248 0.6 1 19 229 90 217 0.6 1 25 192 91 175 0.6 1 14 161 92 202 0.6 1 14 188 93 255 0.6 1 23 232 94 223 0.6 1 20 203 95 132 0.6 1 12 120 96 143 0.6 1 15 128 97 157 0.6 1 19 138 98 143 0.6 1 9 134 99 207 0.6 1 22 185 100 179 0.6 1 17 162 101 103 0.6 1 6 97 102 189 0.6 1 18 171 103 94 0.6 1 9 85 104 65 0.6 1 4 61 105 41 0.6 1 3 38 106 29 0.6 1 2 27 107 34 0.6 1 3 31 108 18 0.6 1 3 15 109 26 0.6 1 2 24 110 52 0.6 1 1 51 111 3 0.6 1 0 3 112 6 0.6 1 3 3 113 3 0.6 1 2 1 114 6 0.6 1 3 3 115 6 0.6 1 4 2 116 4 0.6 1 3 1 117 9 0.6 1 7 2 118 6 0.6 1 5 1 119 1 0.6 1 0 1 120 3 0.6 1 2 1 121 2 0.6 1 2 122 6 0.6 1 4 2 123 6 0.6 1 5 1 124 2 0.6 1 2 125 12 0.6 1 9 3 126 22 0.6 1 18 4 127 25 0.6 1 25 128 36 0.6 1 32 4 129 48 0.6 1 42 6 130 47 0.6 1 41 6 131 44 0.6 1 41 3 132 49 0.6 1 47 2 133 72 0.6 1 66 6 134 88 0.6 1 83 5 135 273 0.6 1 244 29 136 731 0.6 1 675 56 137 40930 0.6 1 39967 963 138 567357 0.6 1 557358 9999 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041628_val_2.fq.gz ============================================= 37837628 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1560698 (4.1%) 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: 37837628 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 708298 (1.87%)