SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041591_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/20201120/tmp/a594373e-5572-11eb-9e34-6c92bfc12f32/trimmed/RRBS20A041591_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 517.63 s (24 us/read; 2.51 M reads/minute). === Summary === Total reads processed: 21,663,739 Reads with adapters: 8,747,950 (40.4%) Reads written (passing filters): 21,663,739 (100.0%) Total basepairs processed: 2,234,158,004 bp Total written (filtered): 2,187,162,350 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8747950 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.4% C: 67.2% G: 4.2% T: 7.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8338375 5415934.8 0 8338375 2 85222 1353983.7 0 85222 3 10295 338495.9 0 10295 4 6396 84624.0 0 6396 5 1689 21156.0 0 1689 6 769 5289.0 0 769 7 1397 1322.2 0 1397 8 599 330.6 0 599 9 271 82.6 0 227 44 10 3342 20.7 1 671 2671 11 131 5.2 1 17 114 12 2603 1.3 1 435 2168 13 624 0.3 1 56 568 14 657 0.3 1 35 622 15 246 0.3 1 10 236 16 321 0.3 1 27 294 17 714 0.3 1 38 676 18 234 0.3 1 18 216 19 622 0.3 1 45 577 20 416 0.3 1 29 387 21 56 0.3 1 15 41 22 380 0.3 1 28 352 23 620 0.3 1 33 587 24 1418 0.3 1 83 1335 25 445 0.3 1 18 427 26 713 0.3 1 40 673 27 273 0.3 1 13 260 28 552 0.3 1 55 497 29 58 0.3 1 4 54 30 467 0.3 1 45 422 31 440 0.3 1 43 397 32 466 0.3 1 35 431 33 1074 0.3 1 70 1004 34 343 0.3 1 26 317 35 723 0.3 1 57 666 36 96 0.3 1 10 86 37 586 0.3 1 32 554 38 168 0.3 1 11 157 39 213 0.3 1 8 205 40 139 0.3 1 14 125 41 334 0.3 1 16 318 42 528 0.3 1 33 495 43 215 0.3 1 16 199 44 420 0.3 1 26 394 45 812 0.3 1 51 761 46 307 0.3 1 22 285 47 118 0.3 1 8 110 48 567 0.3 1 51 516 49 278 0.3 1 21 257 50 507 0.3 1 45 462 51 588 0.3 1 46 542 52 554 0.3 1 43 511 53 101 0.3 1 9 92 54 287 0.3 1 13 274 55 217 0.3 1 23 194 56 56 0.3 1 2 54 57 205 0.3 1 13 192 58 469 0.3 1 31 438 59 212 0.3 1 21 191 60 301 0.3 1 34 267 61 438 0.3 1 66 372 62 479 0.3 1 108 371 63 493 0.3 1 105 388 64 159 0.3 1 22 137 65 219 0.3 1 42 177 66 644 0.3 1 40 604 67 314 0.3 1 13 301 68 249 0.3 1 23 226 69 251 0.3 1 31 220 70 232 0.3 1 16 216 71 244 0.3 1 20 224 72 217 0.3 1 26 191 73 160 0.3 1 19 141 74 221 0.3 1 15 206 75 353 0.3 1 38 315 76 382 0.3 1 27 355 77 234 0.3 1 18 216 78 156 0.3 1 6 150 79 175 0.3 1 14 161 80 207 0.3 1 14 193 81 193 0.3 1 8 185 82 228 0.3 1 12 216 83 212 0.3 1 14 198 84 250 0.3 1 24 226 85 271 0.3 1 22 249 86 141 0.3 1 15 126 87 110 0.3 1 10 100 88 109 0.3 1 14 95 89 139 0.3 1 20 119 90 107 0.3 1 15 92 91 70 0.3 1 8 62 92 81 0.3 1 11 70 93 122 0.3 1 8 114 94 112 0.3 1 12 100 95 63 0.3 1 7 56 96 40 0.3 1 3 37 97 44 0.3 1 5 39 98 53 0.3 1 3 50 99 75 0.3 1 8 67 100 36 0.3 1 1 35 101 23 0.3 1 2 21 102 38 0.3 1 1 37 103 28 0.3 1 1 27 104 20 0.3 1 0 20 105 19 0.3 1 1 18 106 10 0.3 1 1 9 107 10 0.3 1 1 9 108 5 0.3 1 0 5 109 9 0.3 1 2 7 110 12 0.3 1 0 12 111 3 0.3 1 0 3 112 1 0.3 1 1 113 1 0.3 1 0 1 114 5 0.3 1 1 4 115 3 0.3 1 2 1 116 3 0.3 1 1 2 117 4 0.3 1 2 2 118 1 0.3 1 1 119 1 0.3 1 1 120 2 0.3 1 2 121 2 0.3 1 1 1 123 2 0.3 1 1 1 124 1 0.3 1 1 125 3 0.3 1 2 1 126 7 0.3 1 7 127 7 0.3 1 7 128 20 0.3 1 16 4 129 15 0.3 1 14 1 130 21 0.3 1 19 2 131 18 0.3 1 13 5 132 11 0.3 1 10 1 133 31 0.3 1 23 8 134 37 0.3 1 33 4 135 101 0.3 1 88 13 136 267 0.3 1 245 22 137 5086 0.3 1 4879 207 138 262611 0.3 1 257540 5071 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041591_val_2.fq.gz ============================================= 21663739 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1076712 (5.0%) 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: 21663739 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 307579 (1.42%)