SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041587_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/20201121/tmp/c2c95316-3f65-11eb-92b7-6c92bfc12dd0/trimmed/RRBS20A041587_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1147.73 s (43 us/read; 1.41 M reads/minute). === Summary === Total reads processed: 26,975,259 Reads with adapters: 9,983,194 (37.0%) Reads written (passing filters): 26,975,259 (100.0%) Total basepairs processed: 2,695,049,748 bp Total written (filtered): 2,610,881,169 bp (96.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9983194 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.9% C: 64.9% G: 6.7% T: 7.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9236807 6743814.8 0 9236807 2 147670 1685953.7 0 147670 3 12624 421488.4 0 12624 4 7600 105372.1 0 7600 5 2526 26343.0 0 2526 6 1251 6585.8 0 1251 7 2239 1646.4 0 2239 8 750 411.6 0 750 9 364 102.9 0 320 44 10 4034 25.7 1 871 3163 11 185 6.4 1 25 160 12 3102 1.6 1 680 2422 13 748 0.4 1 99 649 14 956 0.4 1 80 876 15 360 0.4 1 31 329 16 406 0.4 1 29 377 17 672 0.4 1 31 641 18 271 0.4 1 15 256 19 789 0.4 1 46 743 20 599 0.4 1 38 561 21 84 0.4 1 43 41 22 482 0.4 1 52 430 23 678 0.4 1 51 627 24 1552 0.4 1 87 1465 25 481 0.4 1 33 448 26 874 0.4 1 53 821 27 321 0.4 1 26 295 28 660 0.4 1 53 607 29 57 0.4 1 1 56 30 578 0.4 1 39 539 31 539 0.4 1 41 498 32 521 0.4 1 25 496 33 1379 0.4 1 75 1304 34 365 0.4 1 25 340 35 729 0.4 1 59 670 36 84 0.4 1 2 82 37 713 0.4 1 46 667 38 212 0.4 1 16 196 39 275 0.4 1 24 251 40 269 0.4 1 20 249 41 690 0.4 1 21 669 42 660 0.4 1 28 632 43 235 0.4 1 12 223 44 407 0.4 1 24 383 45 945 0.4 1 77 868 46 433 0.4 1 21 412 47 196 0.4 1 7 189 48 663 0.4 1 45 618 49 362 0.4 1 29 333 50 485 0.4 1 28 457 51 731 0.4 1 67 664 52 774 0.4 1 63 711 53 84 0.4 1 4 80 54 367 0.4 1 29 338 55 291 0.4 1 29 262 56 62 0.4 1 2 60 57 289 0.4 1 18 271 58 599 0.4 1 42 557 59 337 0.4 1 42 295 60 514 0.4 1 73 441 61 628 0.4 1 135 493 62 1049 0.4 1 347 702 63 837 0.4 1 181 656 64 290 0.4 1 30 260 65 296 0.4 1 37 259 66 605 0.4 1 60 545 67 390 0.4 1 45 345 68 401 0.4 1 39 362 69 338 0.4 1 33 305 70 311 0.4 1 35 276 71 272 0.4 1 24 248 72 285 0.4 1 26 259 73 220 0.4 1 19 201 74 232 0.4 1 10 222 75 789 0.4 1 82 707 76 544 0.4 1 23 521 77 397 0.4 1 30 367 78 250 0.4 1 13 237 79 258 0.4 1 12 246 80 333 0.4 1 24 309 81 225 0.4 1 14 211 82 208 0.4 1 5 203 83 299 0.4 1 18 281 84 384 0.4 1 27 357 85 283 0.4 1 18 265 86 224 0.4 1 20 204 87 157 0.4 1 15 142 88 175 0.4 1 17 158 89 149 0.4 1 15 134 90 145 0.4 1 7 138 91 115 0.4 1 9 106 92 120 0.4 1 9 111 93 166 0.4 1 18 148 94 177 0.4 1 14 163 95 100 0.4 1 10 90 96 95 0.4 1 5 90 97 114 0.4 1 12 102 98 90 0.4 1 7 83 99 171 0.4 1 17 154 100 157 0.4 1 15 142 101 89 0.4 1 5 84 102 177 0.4 1 22 155 103 50 0.4 1 6 44 104 48 0.4 1 3 45 105 35 0.4 1 4 31 106 27 0.4 1 4 23 107 20 0.4 1 4 16 108 15 0.4 1 2 13 109 31 0.4 1 10 21 110 37 0.4 1 4 33 111 6 0.4 1 3 3 112 6 0.4 1 3 3 113 5 0.4 1 4 1 114 12 0.4 1 6 6 115 11 0.4 1 11 116 9 0.4 1 6 3 117 9 0.4 1 9 118 1 0.4 1 1 119 10 0.4 1 9 1 120 5 0.4 1 3 2 121 7 0.4 1 6 1 122 6 0.4 1 4 2 123 12 0.4 1 9 3 124 10 0.4 1 9 1 125 20 0.4 1 17 3 126 29 0.4 1 22 7 127 43 0.4 1 39 4 128 61 0.4 1 58 3 129 46 0.4 1 40 6 130 54 0.4 1 48 6 131 56 0.4 1 51 5 132 73 0.4 1 59 14 133 126 0.4 1 102 24 134 192 0.4 1 169 23 135 528 0.4 1 467 61 136 1272 0.4 1 1171 101 137 22843 0.4 1 22031 812 138 501002 0.4 1 491456 9546 139 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041587_val_2.fq.gz ============================================= 26975259 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1309483 (4.9%) 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: 26975259 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 611114 (2.27%)