SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041684_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/raw_data/cup/BS_workflow/20201115/tmp/4556e7ae-3e8e-11eb-aa66-b4055d0383c6/trimmed/RRBS20A041684_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 484.85 s (24 us/read; 2.54 M reads/minute). === Summary === Total reads processed: 20,534,529 Reads with adapters: 8,067,119 (39.3%) Reads written (passing filters): 20,534,529 (100.0%) Total basepairs processed: 2,056,070,469 bp Total written (filtered): 2,030,645,887 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8067119 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.6% C: 71.4% G: 2.6% T: 6.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7829710 5133632.2 0 7829710 2 57883 1283408.1 0 57883 3 9928 320852.0 0 9928 4 5843 80213.0 0 5843 5 1859 20053.3 0 1859 6 888 5013.3 0 888 7 1309 1253.3 0 1309 8 891 313.3 0 891 9 481 78.3 0 441 40 10 3296 19.6 1 843 2453 11 130 4.9 1 15 115 12 2436 1.2 1 561 1875 13 671 0.3 1 74 597 14 935 0.3 1 82 853 15 366 0.3 1 31 335 16 388 0.3 1 38 350 17 835 0.3 1 83 752 18 354 0.3 1 35 319 19 974 0.3 1 105 869 20 734 0.3 1 78 656 21 33 0.3 1 7 26 22 569 0.3 1 48 521 23 720 0.3 1 53 667 24 1705 0.3 1 135 1570 25 692 0.3 1 52 640 26 1227 0.3 1 102 1125 27 430 0.3 1 43 387 28 666 0.3 1 70 596 29 64 0.3 1 2 62 30 584 0.3 1 43 541 31 639 0.3 1 56 583 32 640 0.3 1 53 587 33 1890 0.3 1 203 1687 34 505 0.3 1 58 447 35 642 0.3 1 49 593 36 132 0.3 1 16 116 37 1026 0.3 1 106 920 38 222 0.3 1 31 191 39 293 0.3 1 35 258 40 219 0.3 1 28 191 41 368 0.3 1 34 334 42 621 0.3 1 71 550 43 335 0.3 1 33 302 44 502 0.3 1 50 452 45 1190 0.3 1 120 1070 46 564 0.3 1 62 502 47 155 0.3 1 11 144 48 647 0.3 1 82 565 49 389 0.3 1 44 345 50 731 0.3 1 93 638 51 711 0.3 1 81 630 52 576 0.3 1 53 523 53 83 0.3 1 9 74 54 451 0.3 1 46 405 55 288 0.3 1 26 262 56 53 0.3 1 10 43 57 277 0.3 1 21 256 58 798 0.3 1 105 693 59 388 0.3 1 38 350 60 573 0.3 1 69 504 61 713 0.3 1 95 618 62 863 0.3 1 99 764 63 794 0.3 1 101 693 64 214 0.3 1 27 187 65 195 0.3 1 12 183 66 416 0.3 1 39 377 67 512 0.3 1 70 442 68 395 0.3 1 44 351 69 385 0.3 1 41 344 70 370 0.3 1 28 342 71 366 0.3 1 31 335 72 339 0.3 1 29 310 73 334 0.3 1 36 298 74 302 0.3 1 20 282 75 478 0.3 1 53 425 76 484 0.3 1 56 428 77 452 0.3 1 48 404 78 272 0.3 1 25 247 79 309 0.3 1 33 276 80 313 0.3 1 39 274 81 253 0.3 1 20 233 82 311 0.3 1 25 286 83 340 0.3 1 31 309 84 371 0.3 1 45 326 85 388 0.3 1 46 342 86 289 0.3 1 41 248 87 221 0.3 1 25 196 88 252 0.3 1 27 225 89 273 0.3 1 40 233 90 206 0.3 1 31 175 91 156 0.3 1 14 142 92 136 0.3 1 12 124 93 226 0.3 1 32 194 94 194 0.3 1 18 176 95 134 0.3 1 13 121 96 98 0.3 1 5 93 97 134 0.3 1 9 125 98 75 0.3 1 6 69 99 103 0.3 1 12 91 100 92 0.3 1 9 83 101 53 0.3 1 7 46 102 89 0.3 1 8 81 103 92 0.3 1 14 78 104 38 0.3 1 3 35 105 59 0.3 1 6 53 106 35 0.3 1 2 33 107 23 0.3 1 5 18 108 19 0.3 1 4 15 109 21 0.3 1 3 18 110 46 0.3 1 7 39 111 6 0.3 1 2 4 112 4 0.3 1 0 4 113 2 0.3 1 1 1 114 1 0.3 1 0 1 115 1 0.3 1 0 1 116 4 0.3 1 0 4 118 2 0.3 1 1 1 122 1 0.3 1 0 1 127 2 0.3 1 2 128 1 0.3 1 1 129 1 0.3 1 1 130 2 0.3 1 2 131 1 0.3 1 1 133 2 0.3 1 2 134 7 0.3 1 7 135 20 0.3 1 19 1 136 69 0.3 1 66 3 137 11419 0.3 1 11218 201 138 99832 0.3 1 98335 1497 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041684_val_2.fq.gz ============================================= 20534529 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1091831 (5.3%) 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: 20534529 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 178491 (0.87%)