SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041584_val_1.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/20201110/tmp/c9157a74-5581-11eb-8d91-6c92bfc39756/trimmed/RRBS20A041584_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 386.79 s (22 us/read; 2.70 M reads/minute). === Summary === Total reads processed: 17,379,964 Reads with adapters: 6,806,744 (39.2%) Reads written (passing filters): 17,379,964 (100.0%) Total basepairs processed: 1,696,276,533 bp Total written (filtered): 1,654,861,304 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6806744 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 0.9% G: 20.5% T: 48.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4811764 4344991.0 0 4811764 2 1309018 1086247.8 0 1309018 3 326713 271561.9 0 326713 4 74186 67890.5 0 74186 5 3274 16972.6 0 3274 6 1647 4243.2 0 1647 7 1632 1060.8 0 1632 8 637 265.2 0 637 9 1247 66.3 0 1025 222 10 1719 16.6 1 419 1300 11 1202 4.1 1 118 1084 12 438 1.0 1 58 380 13 474 0.3 1 39 435 14 1204 0.3 1 119 1085 15 774 0.3 1 66 708 16 2611 0.3 1 215 2396 17 2435 0.3 1 212 2223 18 883 0.3 1 312 571 19 44 0.3 1 6 38 20 408 0.3 1 34 374 21 73 0.3 1 9 64 22 118 0.3 1 10 108 23 395 0.3 1 34 361 24 1959 0.3 1 167 1792 25 754 0.3 1 85 669 26 288 0.3 1 22 266 27 555 0.3 1 47 508 28 1330 0.3 1 96 1234 29 1586 0.3 1 132 1454 30 268 0.3 1 29 239 31 83 0.3 1 8 75 32 504 0.3 1 48 456 33 1277 0.3 1 122 1155 34 1646 0.3 1 158 1488 35 623 0.3 1 53 570 36 600 0.3 1 55 545 37 1474 0.3 1 158 1316 38 349 0.3 1 29 320 39 221 0.3 1 22 199 40 1256 0.3 1 123 1133 41 547 0.3 1 42 505 42 1171 0.3 1 105 1066 43 2135 0.3 1 174 1961 44 344 0.3 1 23 321 45 760 0.3 1 64 696 46 201 0.3 1 16 185 47 429 0.3 1 36 393 48 1396 0.3 1 110 1286 49 199 0.3 1 10 189 50 613 0.3 1 60 553 51 264 0.3 1 27 237 52 173 0.3 1 5 168 53 394 0.3 1 40 354 54 1143 0.3 1 103 1040 55 815 0.3 1 82 733 56 486 0.3 1 46 440 57 471 0.3 1 73 398 58 374 0.3 1 38 336 59 217 0.3 1 23 194 60 327 0.3 1 40 287 61 493 0.3 1 48 445 62 2317 0.3 1 181 2136 63 377 0.3 1 57 320 64 76 0.3 1 6 70 65 59 0.3 1 2 57 66 899 0.3 1 80 819 67 174 0.3 1 11 163 68 643 0.3 1 52 591 69 790 0.3 1 70 720 70 1248 0.3 1 120 1128 71 270 0.3 1 25 245 72 143 0.3 1 16 127 73 307 0.3 1 28 279 74 354 0.3 1 35 319 75 390 0.3 1 34 356 76 436 0.3 1 39 397 77 550 0.3 1 53 497 78 605 0.3 1 47 558 79 484 0.3 1 49 435 80 621 0.3 1 60 561 81 553 0.3 1 39 514 82 540 0.3 1 41 499 83 695 0.3 1 60 635 84 556 0.3 1 58 498 85 836 0.3 1 67 769 86 505 0.3 1 34 471 87 377 0.3 1 32 345 88 386 0.3 1 37 349 89 463 0.3 1 45 418 90 427 0.3 1 34 393 91 434 0.3 1 21 413 92 329 0.3 1 26 303 93 581 0.3 1 42 539 94 987 0.3 1 72 915 95 325 0.3 1 27 298 96 244 0.3 1 14 230 97 639 0.3 1 42 597 98 273 0.3 1 18 255 99 163 0.3 1 10 153 100 169 0.3 1 14 155 101 158 0.3 1 9 149 102 240 0.3 1 24 216 103 103 0.3 1 11 92 104 75 0.3 1 10 65 105 68 0.3 1 7 61 106 60 0.3 1 5 55 107 30 0.3 1 5 25 108 12 0.3 1 3 9 109 15 0.3 1 2 13 110 10 0.3 1 1 9 111 6 0.3 1 2 4 112 4 0.3 1 0 4 113 2 0.3 1 1 1 114 2 0.3 1 1 1 116 1 0.3 1 1 118 1 0.3 1 0 1 121 2 0.3 1 2 122 2 0.3 1 2 123 3 0.3 1 3 125 4 0.3 1 4 127 5 0.3 1 3 2 128 4 0.3 1 2 2 129 4 0.3 1 3 1 130 6 0.3 1 3 3 131 11 0.3 1 7 4 132 9 0.3 1 6 3 133 55 0.3 1 33 22 134 62 0.3 1 53 9 135 59 0.3 1 44 15 136 129 0.3 1 97 32 137 4110 0.3 1 3934 176 138 210638 0.3 1 205145 5493 139 1 0.3 1 0 1 140 7 0.3 1 0 7 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041584_val_1.fq.gz ============================================= 17379964 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 765724 (4.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6806740 (39.2%)