SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041688_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/4b3c370a-3e8e-11eb-9c84-6c92bfc128e4/trimmed/RRBS20A041688_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 993.93 s (25 us/read; 2.39 M reads/minute). === Summary === Total reads processed: 39,575,012 Reads with adapters: 15,576,761 (39.4%) Reads written (passing filters): 39,575,012 (100.0%) Total basepairs processed: 4,120,021,515 bp Total written (filtered): 4,025,096,028 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15576761 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 57.0% G: 4.9% T: 10.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14786526 9893753.0 0 14786526 2 138398 2473438.2 0 138398 3 15746 618359.6 0 15746 4 9841 154589.9 0 9841 5 2607 38647.5 0 2607 6 1455 9661.9 0 1455 7 2266 2415.5 0 2266 8 1163 603.9 0 1163 9 572 151.0 0 511 61 10 5176 37.7 1 1203 3973 11 190 9.4 1 19 171 12 4376 2.4 1 844 3532 13 950 0.6 1 107 843 14 1171 0.6 1 69 1102 15 403 0.6 1 25 378 16 471 0.6 1 42 429 17 936 0.6 1 43 893 18 381 0.6 1 12 369 19 1122 0.6 1 54 1068 20 807 0.6 1 50 757 21 76 0.6 1 27 49 22 705 0.6 1 49 656 23 1087 0.6 1 73 1014 24 2492 0.6 1 177 2315 25 786 0.6 1 52 734 26 1499 0.6 1 70 1429 27 466 0.6 1 21 445 28 813 0.6 1 50 763 29 70 0.6 1 6 64 30 732 0.6 1 48 684 31 799 0.6 1 50 749 32 858 0.6 1 60 798 33 2293 0.6 1 163 2130 34 502 0.6 1 36 466 35 851 0.6 1 51 800 36 121 0.6 1 9 112 37 1056 0.6 1 72 984 38 219 0.6 1 12 207 39 348 0.6 1 26 322 40 219 0.6 1 14 205 41 614 0.6 1 34 580 42 743 0.6 1 43 700 43 322 0.6 1 19 303 44 535 0.6 1 35 500 45 1384 0.6 1 119 1265 46 537 0.6 1 28 509 47 146 0.6 1 7 139 48 1011 0.6 1 91 920 49 373 0.6 1 25 348 50 696 0.6 1 56 640 51 908 0.6 1 77 831 52 927 0.6 1 76 851 53 133 0.6 1 8 125 54 498 0.6 1 37 461 55 303 0.6 1 24 279 56 64 0.6 1 3 61 57 324 0.6 1 24 300 58 747 0.6 1 62 685 59 383 0.6 1 34 349 60 524 0.6 1 50 474 61 661 0.6 1 76 585 62 840 0.6 1 152 688 63 752 0.6 1 109 643 64 285 0.6 1 22 263 65 251 0.6 1 27 224 66 537 0.6 1 36 501 67 426 0.6 1 37 389 68 433 0.6 1 31 402 69 399 0.6 1 33 366 70 365 0.6 1 38 327 71 376 0.6 1 30 346 72 296 0.6 1 22 274 73 302 0.6 1 24 278 74 359 0.6 1 18 341 75 709 0.6 1 45 664 76 711 0.6 1 49 662 77 428 0.6 1 25 403 78 296 0.6 1 17 279 79 305 0.6 1 19 286 80 321 0.6 1 21 300 81 290 0.6 1 22 268 82 292 0.6 1 23 269 83 365 0.6 1 21 344 84 440 0.6 1 27 413 85 420 0.6 1 36 384 86 271 0.6 1 11 260 87 237 0.6 1 18 219 88 193 0.6 1 20 173 89 240 0.6 1 11 229 90 191 0.6 1 11 180 91 164 0.6 1 12 152 92 131 0.6 1 9 122 93 187 0.6 1 8 179 94 167 0.6 1 13 154 95 95 0.6 1 7 88 96 116 0.6 1 7 109 97 112 0.6 1 3 109 98 96 0.6 1 7 89 99 172 0.6 1 24 148 100 126 0.6 1 6 120 101 80 0.6 1 7 73 102 122 0.6 1 9 113 103 62 0.6 1 6 56 104 55 0.6 1 5 50 105 46 0.6 1 8 38 106 28 0.6 1 4 24 107 31 0.6 1 2 29 108 28 0.6 1 1 27 109 28 0.6 1 1 27 110 33 0.6 1 3 30 111 13 0.6 1 2 11 112 10 0.6 1 5 5 113 4 0.6 1 2 2 114 7 0.6 1 3 4 115 3 0.6 1 3 116 8 0.6 1 8 117 7 0.6 1 2 5 118 6 0.6 1 5 1 119 6 0.6 1 3 3 120 7 0.6 1 5 2 121 3 0.6 1 0 3 122 4 0.6 1 2 2 123 8 0.6 1 6 2 124 9 0.6 1 7 2 125 6 0.6 1 4 2 126 11 0.6 1 9 2 127 19 0.6 1 15 4 128 38 0.6 1 31 7 129 25 0.6 1 23 2 130 28 0.6 1 23 5 131 20 0.6 1 15 5 132 37 0.6 1 31 6 133 48 0.6 1 39 9 134 57 0.6 1 50 7 135 184 0.6 1 167 17 136 444 0.6 1 392 52 137 7750 0.6 1 7430 320 138 552407 0.6 1 542334 10073 139 1 0.6 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041688_val_2.fq.gz ============================================= 39575012 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1766248 (4.5%) 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: 39575012 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 673682 (1.70%)