SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041625_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/raw_data/cup/BS_workflow/20201121/tmp/c32f3cb2-3f65-11eb-a561-6c92bfc1302e/trimmed/RRBS20A041625_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 471.68 s (21 us/read; 2.81 M reads/minute). === Summary === Total reads processed: 22,127,674 Reads with adapters: 9,860,350 (44.6%) Reads written (passing filters): 22,127,674 (100.0%) Total basepairs processed: 2,244,505,741 bp Total written (filtered): 2,005,040,635 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9860350 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.3% C: 17.5% G: 16.7% T: 40.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5986129 5531918.5 0 5986129 2 1692442 1382979.6 0 1692442 3 373769 345744.9 0 373769 4 86140 86436.2 0 86140 5 5624 21609.1 0 5624 6 2286 5402.3 0 2286 7 1318 1350.6 0 1318 8 1336 337.6 0 1336 9 1921 84.4 0 1673 248 10 2150 21.1 1 729 1421 11 1687 5.3 1 211 1476 12 600 1.3 1 72 528 13 647 0.3 1 81 566 14 1269 0.3 1 196 1073 15 1436 0.3 1 251 1185 16 3948 0.3 1 1658 2290 17 4206 0.3 1 602 3604 18 1381 0.3 1 248 1133 19 92 0.3 1 17 75 20 749 0.3 1 139 610 21 105 0.3 1 10 95 22 76 0.3 1 5 71 23 600 0.3 1 95 505 24 1812 0.3 1 313 1499 25 955 0.3 1 137 818 26 264 0.3 1 38 226 27 938 0.3 1 160 778 28 2078 0.3 1 321 1757 29 1860 0.3 1 286 1574 30 421 0.3 1 65 356 31 66 0.3 1 5 61 32 820 0.3 1 137 683 33 1269 0.3 1 204 1065 34 1352 0.3 1 210 1142 35 2176 0.3 1 387 1789 36 927 0.3 1 151 776 37 508 0.3 1 162 346 38 1216 0.3 1 153 1063 39 480 0.3 1 80 400 40 1808 0.3 1 237 1571 41 1288 0.3 1 169 1119 42 1297 0.3 1 197 1100 43 2119 0.3 1 291 1828 44 291 0.3 1 32 259 45 1133 0.3 1 146 987 46 325 0.3 1 45 280 47 619 0.3 1 55 564 48 2189 0.3 1 339 1850 49 245 0.3 1 29 216 50 816 0.3 1 127 689 51 268 0.3 1 43 225 52 226 0.3 1 34 192 53 536 0.3 1 90 446 54 2312 0.3 1 312 2000 55 1167 0.3 1 170 997 56 566 0.3 1 78 488 57 938 0.3 1 131 807 58 548 0.3 1 82 466 59 224 0.3 1 32 192 60 485 0.3 1 62 423 61 623 0.3 1 94 529 62 1652 0.3 1 298 1354 63 451 0.3 1 74 377 64 60 0.3 1 16 44 65 50 0.3 1 7 43 66 309 0.3 1 48 261 67 260 0.3 1 22 238 68 909 0.3 1 113 796 69 979 0.3 1 144 835 70 1677 0.3 1 262 1415 71 615 0.3 1 84 531 72 246 0.3 1 37 209 73 348 0.3 1 48 300 74 350 0.3 1 40 310 75 442 0.3 1 65 377 76 448 0.3 1 85 363 77 513 0.3 1 83 430 78 441 0.3 1 54 387 79 426 0.3 1 66 360 80 611 0.3 1 86 525 81 409 0.3 1 48 361 82 492 0.3 1 66 426 83 526 0.3 1 73 453 84 395 0.3 1 40 355 85 423 0.3 1 42 381 86 738 0.3 1 116 622 87 373 0.3 1 52 321 88 317 0.3 1 53 264 89 366 0.3 1 49 317 90 275 0.3 1 36 239 91 272 0.3 1 33 239 92 317 0.3 1 47 270 93 1718 0.3 1 160 1558 94 2044 0.3 1 242 1802 95 612 0.3 1 80 532 96 357 0.3 1 52 305 97 2261 0.3 1 242 2019 98 328 0.3 1 45 283 99 185 0.3 1 28 157 100 183 0.3 1 18 165 101 237 0.3 1 33 204 102 459 0.3 1 71 388 103 137 0.3 1 23 114 104 75 0.3 1 10 65 105 104 0.3 1 16 88 106 108 0.3 1 18 90 107 59 0.3 1 13 46 108 20 0.3 1 6 14 109 56 0.3 1 14 42 110 120 0.3 1 12 108 111 26 0.3 1 10 16 112 19 0.3 1 6 13 113 10 0.3 1 6 4 114 42 0.3 1 12 30 115 9 0.3 1 6 3 116 7 0.3 1 6 1 117 5 0.3 1 2 3 118 8 0.3 1 5 3 119 3 0.3 1 3 120 8 0.3 1 7 1 121 10 0.3 1 8 2 122 16 0.3 1 14 2 123 19 0.3 1 13 6 124 26 0.3 1 18 8 125 29 0.3 1 24 5 126 22 0.3 1 19 3 127 35 0.3 1 27 8 128 41 0.3 1 32 9 129 42 0.3 1 29 13 130 59 0.3 1 45 14 131 83 0.3 1 66 17 132 148 0.3 1 115 33 133 323 0.3 1 232 91 134 518 0.3 1 428 90 135 616 0.3 1 519 97 136 1064 0.3 1 903 161 137 25485 0.3 1 24253 1232 138 1599818 0.3 1 1558317 41501 139 6 0.3 1 0 6 140 23 0.3 1 1 22 143 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041625_val_1.fq.gz ============================================= 22127674 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 821002 (3.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 9860309 (44.6%)