SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041588_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/20201115/tmp/44fb8ac6-3e8e-11eb-b4e4-6c92bfc12f0e/trimmed/RRBS20A041588_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 511.21 s (22 us/read; 2.71 M reads/minute). === Summary === Total reads processed: 23,052,481 Reads with adapters: 10,682,119 (46.3%) Reads written (passing filters): 23,052,481 (100.0%) Total basepairs processed: 2,458,685,289 bp Total written (filtered): 2,226,537,041 bp (90.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10682119 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.4% C: 15.8% G: 16.4% T: 41.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6635009 5763120.2 0 6635009 2 1835137 1440780.1 0 1835137 3 435316 360195.0 0 435316 4 94320 90048.8 0 94320 5 7357 22512.2 0 7357 6 4928 5628.0 0 4928 7 3493 1407.0 0 3493 8 3155 351.8 0 3155 9 4043 87.9 0 3704 339 10 4006 22.0 1 2155 1851 11 2201 5.5 1 378 1823 12 980 1.4 1 167 813 13 898 0.3 1 147 751 14 1756 0.3 1 263 1493 15 1650 0.3 1 290 1360 16 4832 0.3 1 1680 3152 17 4719 0.3 1 797 3922 18 1968 0.3 1 406 1562 19 107 0.3 1 9 98 20 887 0.3 1 163 724 21 87 0.3 1 9 78 22 157 0.3 1 30 127 23 854 0.3 1 128 726 24 2708 0.3 1 467 2241 25 1240 0.3 1 221 1019 26 282 0.3 1 46 236 27 1168 0.3 1 179 989 28 2323 0.3 1 350 1973 29 2461 0.3 1 391 2070 30 615 0.3 1 109 506 31 99 0.3 1 10 89 32 1012 0.3 1 161 851 33 1664 0.3 1 242 1422 34 1670 0.3 1 350 1320 35 2788 0.3 1 471 2317 36 1121 0.3 1 165 956 37 540 0.3 1 105 435 38 1704 0.3 1 251 1453 39 713 0.3 1 97 616 40 2200 0.3 1 317 1883 41 1774 0.3 1 270 1504 42 1877 0.3 1 291 1586 43 2426 0.3 1 415 2011 44 402 0.3 1 60 342 45 1344 0.3 1 234 1110 46 400 0.3 1 54 346 47 787 0.3 1 118 669 48 2720 0.3 1 479 2241 49 297 0.3 1 35 262 50 817 0.3 1 160 657 51 302 0.3 1 45 257 52 275 0.3 1 47 228 53 617 0.3 1 101 516 54 1934 0.3 1 318 1616 55 1483 0.3 1 274 1209 56 679 0.3 1 100 579 57 904 0.3 1 160 744 58 562 0.3 1 72 490 59 270 0.3 1 42 228 60 456 0.3 1 69 387 61 649 0.3 1 87 562 62 1892 0.3 1 329 1563 63 402 0.3 1 63 339 64 99 0.3 1 8 91 65 56 0.3 1 4 52 66 286 0.3 1 46 240 67 186 0.3 1 17 169 68 882 0.3 1 137 745 69 986 0.3 1 148 838 70 1523 0.3 1 213 1310 71 445 0.3 1 70 375 72 196 0.3 1 26 170 73 542 0.3 1 73 469 74 425 0.3 1 73 352 75 505 0.3 1 79 426 76 529 0.3 1 88 441 77 641 0.3 1 117 524 78 552 0.3 1 70 482 79 652 0.3 1 113 539 80 831 0.3 1 137 694 81 583 0.3 1 64 519 82 606 0.3 1 72 534 83 624 0.3 1 100 524 84 455 0.3 1 58 397 85 576 0.3 1 96 480 86 580 0.3 1 76 504 87 367 0.3 1 53 314 88 366 0.3 1 51 315 89 479 0.3 1 62 417 90 296 0.3 1 48 248 91 351 0.3 1 49 302 92 328 0.3 1 34 294 93 1308 0.3 1 169 1139 94 2238 0.3 1 219 2019 95 618 0.3 1 72 546 96 300 0.3 1 41 259 97 2107 0.3 1 243 1864 98 286 0.3 1 31 255 99 152 0.3 1 17 135 100 177 0.3 1 20 157 101 230 0.3 1 43 187 102 387 0.3 1 56 331 103 136 0.3 1 20 116 104 84 0.3 1 13 71 105 97 0.3 1 13 84 106 100 0.3 1 24 76 107 44 0.3 1 9 35 108 30 0.3 1 6 24 109 29 0.3 1 8 21 110 127 0.3 1 25 102 111 21 0.3 1 5 16 112 13 0.3 1 8 5 113 4 0.3 1 4 114 9 0.3 1 3 6 115 5 0.3 1 5 116 3 0.3 1 2 1 117 5 0.3 1 3 2 118 6 0.3 1 4 2 119 4 0.3 1 3 1 120 4 0.3 1 2 2 121 11 0.3 1 8 3 122 8 0.3 1 5 3 123 8 0.3 1 4 4 124 9 0.3 1 7 2 125 10 0.3 1 7 3 126 11 0.3 1 8 3 127 16 0.3 1 11 5 128 20 0.3 1 15 5 129 25 0.3 1 17 8 130 35 0.3 1 28 7 131 56 0.3 1 43 13 132 66 0.3 1 44 22 133 226 0.3 1 169 57 134 506 0.3 1 413 93 135 489 0.3 1 389 100 136 760 0.3 1 644 116 137 15573 0.3 1 14475 1098 138 1545365 0.3 1 1501179 44186 139 3 0.3 1 1 2 140 14 0.3 1 0 14 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041588_val_1.fq.gz ============================================= 23052481 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 883794 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10682115 (46.3%)