SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041687_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/20201120/tmp/a6f6756a-5572-11eb-976b-6c92bfc12788/trimmed/RRBS20A041687_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 435.12 s (22 us/read; 2.67 M reads/minute). === Summary === Total reads processed: 19,375,386 Reads with adapters: 8,771,307 (45.3%) Reads written (passing filters): 19,375,386 (100.0%) Total basepairs processed: 2,042,849,397 bp Total written (filtered): 1,944,441,432 bp (95.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8771307 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 1.0% G: 25.4% T: 43.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5889294 4843846.5 0 5889294 2 1566297 1210961.6 0 1566297 3 456897 302740.4 0 456897 4 92037 75685.1 0 92037 5 14586 18921.3 0 14586 6 9642 4730.3 0 9642 7 9312 1182.6 0 9312 8 8719 295.6 0 8719 9 9271 73.9 0 8877 394 10 9165 18.5 1 6396 2769 11 3337 4.6 1 566 2771 12 1501 1.2 1 305 1196 13 1552 0.3 1 266 1286 14 2161 0.3 1 331 1830 15 1670 0.3 1 265 1405 16 4019 0.3 1 651 3368 17 6027 0.3 1 2204 3823 18 7565 0.3 1 5094 2471 19 201 0.3 1 52 149 20 1346 0.3 1 324 1022 21 114 0.3 1 16 98 22 197 0.3 1 25 172 23 1067 0.3 1 168 899 24 3146 0.3 1 614 2532 25 1321 0.3 1 277 1044 26 466 0.3 1 61 405 27 1459 0.3 1 274 1185 28 2819 0.3 1 506 2313 29 2910 0.3 1 526 2384 30 763 0.3 1 140 623 31 171 0.3 1 20 151 32 1100 0.3 1 199 901 33 1988 0.3 1 330 1658 34 1934 0.3 1 327 1607 35 2737 0.3 1 482 2255 36 1125 0.3 1 196 929 37 734 0.3 1 136 598 38 2196 0.3 1 424 1772 39 903 0.3 1 146 757 40 2515 0.3 1 390 2125 41 1898 0.3 1 331 1567 42 1650 0.3 1 262 1388 43 2794 0.3 1 452 2342 44 462 0.3 1 54 408 45 1378 0.3 1 234 1144 46 480 0.3 1 69 411 47 1025 0.3 1 141 884 48 2562 0.3 1 424 2138 49 270 0.3 1 30 240 50 1344 0.3 1 220 1124 51 389 0.3 1 55 334 52 279 0.3 1 26 253 53 857 0.3 1 144 713 54 2477 0.3 1 451 2026 55 1381 0.3 1 231 1150 56 805 0.3 1 123 682 57 1054 0.3 1 199 855 58 651 0.3 1 93 558 59 284 0.3 1 42 242 60 563 0.3 1 94 469 61 733 0.3 1 76 657 62 1555 0.3 1 267 1288 63 615 0.3 1 115 500 64 93 0.3 1 14 79 65 42 0.3 1 5 37 66 153 0.3 1 21 132 67 280 0.3 1 25 255 68 1038 0.3 1 180 858 69 1220 0.3 1 180 1040 70 2254 0.3 1 382 1872 71 1096 0.3 1 153 943 72 426 0.3 1 57 369 73 337 0.3 1 45 292 74 438 0.3 1 64 374 75 512 0.3 1 82 430 76 648 0.3 1 121 527 77 627 0.3 1 97 530 78 581 0.3 1 87 494 79 594 0.3 1 106 488 80 608 0.3 1 89 519 81 577 0.3 1 110 467 82 687 0.3 1 119 568 83 726 0.3 1 132 594 84 560 0.3 1 76 484 85 632 0.3 1 110 522 86 573 0.3 1 86 487 87 441 0.3 1 58 383 88 372 0.3 1 71 301 89 424 0.3 1 64 360 90 441 0.3 1 69 372 91 345 0.3 1 34 311 92 334 0.3 1 38 296 93 858 0.3 1 137 721 94 944 0.3 1 93 851 95 380 0.3 1 49 331 96 295 0.3 1 39 256 97 668 0.3 1 87 581 98 266 0.3 1 44 222 99 169 0.3 1 23 146 100 158 0.3 1 20 138 101 156 0.3 1 24 132 102 281 0.3 1 54 227 103 121 0.3 1 19 102 104 71 0.3 1 10 61 105 60 0.3 1 8 52 106 57 0.3 1 9 48 107 42 0.3 1 8 34 108 20 0.3 1 5 15 109 9 0.3 1 0 9 110 20 0.3 1 4 16 111 13 0.3 1 4 9 112 4 0.3 1 2 2 113 4 0.3 1 1 3 114 4 0.3 1 2 2 116 10 0.3 1 8 2 117 4 0.3 1 3 1 118 2 0.3 1 2 119 1 0.3 1 1 120 4 0.3 1 3 1 121 1 0.3 1 1 122 5 0.3 1 4 1 123 4 0.3 1 3 1 124 5 0.3 1 3 2 125 3 0.3 1 2 1 126 9 0.3 1 8 1 127 8 0.3 1 7 1 128 14 0.3 1 11 3 129 14 0.3 1 12 2 130 18 0.3 1 16 2 131 15 0.3 1 11 4 132 29 0.3 1 26 3 133 86 0.3 1 64 22 134 129 0.3 1 110 19 135 193 0.3 1 155 38 136 314 0.3 1 277 37 137 17033 0.3 1 16521 512 138 581972 0.3 1 569801 12171 139 1 0.3 1 0 1 140 4 0.3 1 2 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041687_val_1.fq.gz ============================================= 19375386 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 627450 (3.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 8771302 (45.3%)