SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041611_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/20201104_20201106/tmp/5e97a914-48bc-11eb-919a-6c92bfc12ed8/trimmed/RRBS20A041611_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 385.43 s (23 us/read; 2.57 M reads/minute). === Summary === Total reads processed: 16,498,696 Reads with adapters: 6,221,700 (37.7%) Reads written (passing filters): 16,498,696 (100.0%) Total basepairs processed: 1,579,097,668 bp Total written (filtered): 1,565,784,571 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6221700 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.9% C: 78.8% G: 0.9% T: 5.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6056444 4124674.0 0 6056444 2 57873 1031168.5 0 57873 3 10755 257792.1 0 10755 4 10003 64448.0 0 10003 5 2409 16112.0 0 2409 6 1126 4028.0 0 1126 7 1233 1007.0 0 1233 8 1168 251.8 0 1168 9 727 62.9 0 700 27 10 3181 15.7 1 627 2554 11 485 3.9 1 89 396 12 872 1.0 1 149 723 13 732 0.2 1 86 646 14 885 0.2 1 101 784 15 436 0.2 1 42 394 16 714 0.2 1 80 634 17 844 0.2 1 97 747 18 281 0.2 1 30 251 19 722 0.2 1 84 638 20 723 0.2 1 72 651 21 66 0.2 1 6 60 22 112 0.2 1 17 95 23 580 0.2 1 50 530 24 1365 0.2 1 130 1235 25 603 0.2 1 41 562 26 983 0.2 1 89 894 27 754 0.2 1 85 669 28 753 0.2 1 106 647 29 115 0.2 1 14 101 30 155 0.2 1 16 139 31 156 0.2 1 13 143 32 710 0.2 1 87 623 33 1395 0.2 1 174 1221 34 397 0.2 1 38 359 35 374 0.2 1 45 329 36 119 0.2 1 9 110 37 839 0.2 1 87 752 38 306 0.2 1 30 276 39 377 0.2 1 37 340 40 398 0.2 1 35 363 41 313 0.2 1 23 290 42 461 0.2 1 39 422 43 387 0.2 1 45 342 44 420 0.2 1 48 372 45 698 0.2 1 81 617 46 482 0.2 1 53 429 47 209 0.2 1 17 192 48 507 0.2 1 57 450 49 481 0.2 1 51 430 50 496 0.2 1 68 428 51 619 0.2 1 63 556 52 655 0.2 1 66 589 53 114 0.2 1 8 106 54 390 0.2 1 39 351 55 497 0.2 1 61 436 56 99 0.2 1 12 87 57 356 0.2 1 31 325 58 553 0.2 1 56 497 59 437 0.2 1 54 383 60 618 0.2 1 68 550 61 733 0.2 1 63 670 62 932 0.2 1 109 823 63 1024 0.2 1 120 904 64 483 0.2 1 37 446 65 330 0.2 1 37 293 66 739 0.2 1 90 649 67 389 0.2 1 44 345 68 349 0.2 1 27 322 69 358 0.2 1 37 321 70 319 0.2 1 26 293 71 293 0.2 1 30 263 72 332 0.2 1 22 310 73 348 0.2 1 35 313 74 341 0.2 1 37 304 75 746 0.2 1 89 657 76 501 0.2 1 48 453 77 323 0.2 1 32 291 78 239 0.2 1 23 216 79 271 0.2 1 30 241 80 263 0.2 1 24 239 81 264 0.2 1 29 235 82 307 0.2 1 20 287 83 336 0.2 1 43 293 84 359 0.2 1 27 332 85 390 0.2 1 31 359 86 257 0.2 1 25 232 87 204 0.2 1 19 185 88 215 0.2 1 24 191 89 181 0.2 1 22 159 90 208 0.2 1 17 191 91 143 0.2 1 12 131 92 170 0.2 1 18 152 93 189 0.2 1 17 172 94 204 0.2 1 23 181 95 136 0.2 1 13 123 96 184 0.2 1 22 162 97 160 0.2 1 17 143 98 99 0.2 1 12 87 99 153 0.2 1 25 128 100 108 0.2 1 10 98 101 80 0.2 1 4 76 102 122 0.2 1 13 109 103 61 0.2 1 6 55 104 48 0.2 1 4 44 105 49 0.2 1 7 42 106 28 0.2 1 1 27 107 12 0.2 1 1 11 108 12 0.2 1 3 9 109 37 0.2 1 6 31 110 17 0.2 1 0 17 111 5 0.2 1 0 5 112 6 0.2 1 1 5 114 2 0.2 1 1 1 121 1 0.2 1 1 124 1 0.2 1 1 126 2 0.2 1 1 1 127 3 0.2 1 2 1 128 1 0.2 1 0 1 129 2 0.2 1 1 1 130 2 0.2 1 2 131 1 0.2 1 1 132 4 0.2 1 4 133 6 0.2 1 6 134 8 0.2 1 7 1 135 15 0.2 1 12 3 136 64 0.2 1 52 12 137 1753 0.2 1 1660 93 138 34816 0.2 1 33955 861 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041611_val_2.fq.gz ============================================= 16498696 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 985578 (6.0%) 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: 16498696 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 107465 (0.65%)