SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041630_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/20201104_20201106/tmp/602907e6-48bc-11eb-ac9d-6c92bfc12b7e/trimmed/RRBS20A041630_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 439.22 s (24 us/read; 2.48 M reads/minute). === Summary === Total reads processed: 18,184,059 Reads with adapters: 8,065,518 (44.4%) Reads written (passing filters): 18,184,059 (100.0%) Total basepairs processed: 1,826,155,930 bp Total written (filtered): 1,794,225,387 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8065518 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.0% C: 0.7% G: 21.5% T: 45.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5753726 4546014.8 0 5753726 2 1481656 1136503.7 0 1481656 3 384130 284125.9 0 384130 4 86267 71031.5 0 86267 5 9807 17757.9 0 9807 6 5306 4439.5 0 5306 7 4559 1109.9 0 4559 8 4717 277.5 0 4717 9 5763 69.4 0 5523 240 10 6769 17.3 1 3571 3198 11 4348 4.3 1 950 3398 12 2081 1.1 1 491 1590 13 2142 0.3 1 471 1671 14 3152 0.3 1 645 2507 15 2649 0.3 1 523 2126 16 5508 0.3 1 1027 4481 17 8618 0.3 1 1964 6654 18 7447 0.3 1 2725 4722 19 224 0.3 1 33 191 20 2544 0.3 1 599 1945 21 171 0.3 1 24 147 22 312 0.3 1 68 244 23 2219 0.3 1 480 1739 24 5182 0.3 1 1284 3898 25 3120 0.3 1 835 2285 26 557 0.3 1 102 455 27 3158 0.3 1 689 2469 28 5281 0.3 1 1255 4026 29 4352 0.3 1 893 3459 30 1714 0.3 1 463 1251 31 207 0.3 1 38 169 32 2348 0.3 1 468 1880 33 4391 0.3 1 913 3478 34 4876 0.3 1 1021 3855 35 1220 0.3 1 263 957 36 3510 0.3 1 753 2757 37 433 0.3 1 78 355 38 5737 0.3 1 1151 4586 39 4985 0.3 1 1088 3897 40 1801 0.3 1 368 1433 41 6680 0.3 1 1527 5153 42 617 0.3 1 111 506 43 7217 0.3 1 1535 5682 44 1253 0.3 1 253 1000 45 4509 0.3 1 1007 3502 46 1357 0.3 1 277 1080 47 3325 0.3 1 638 2687 48 7607 0.3 1 1804 5803 49 675 0.3 1 122 553 50 3798 0.3 1 825 2973 51 1188 0.3 1 249 939 52 927 0.3 1 194 733 53 3136 0.3 1 796 2340 54 7737 0.3 1 2076 5661 55 5420 0.3 1 1398 4022 56 2571 0.3 1 637 1934 57 5237 0.3 1 1442 3795 58 2825 0.3 1 659 2166 59 1496 0.3 1 346 1150 60 3118 0.3 1 760 2358 61 3746 0.3 1 748 2998 62 10586 0.3 1 2973 7613 63 2767 0.3 1 722 2045 64 273 0.3 1 49 224 65 361 0.3 1 66 295 66 1519 0.3 1 328 1191 67 1220 0.3 1 249 971 68 4063 0.3 1 985 3078 69 4389 0.3 1 1018 3371 70 6747 0.3 1 1574 5173 71 2714 0.3 1 534 2180 72 1351 0.3 1 266 1085 73 1248 0.3 1 266 982 74 1401 0.3 1 385 1016 75 1789 0.3 1 496 1293 76 1883 0.3 1 495 1388 77 2272 0.3 1 540 1732 78 2149 0.3 1 491 1658 79 2121 0.3 1 547 1574 80 2738 0.3 1 628 2110 81 2553 0.3 1 665 1888 82 2748 0.3 1 684 2064 83 3424 0.3 1 851 2573 84 3992 0.3 1 1069 2923 85 5180 0.3 1 1289 3891 86 2439 0.3 1 624 1815 87 1621 0.3 1 418 1203 88 1502 0.3 1 378 1124 89 1615 0.3 1 418 1197 90 1638 0.3 1 432 1206 91 1247 0.3 1 265 982 92 1319 0.3 1 255 1064 93 2626 0.3 1 629 1997 94 5279 0.3 1 1190 4089 95 1485 0.3 1 364 1121 96 1105 0.3 1 251 854 97 5120 0.3 1 1242 3878 98 971 0.3 1 249 722 99 715 0.3 1 178 537 100 645 0.3 1 152 493 101 613 0.3 1 161 452 102 878 0.3 1 239 639 103 497 0.3 1 117 380 104 363 0.3 1 86 277 105 217 0.3 1 43 174 106 230 0.3 1 50 180 107 189 0.3 1 43 146 108 107 0.3 1 33 74 109 65 0.3 1 11 54 110 197 0.3 1 34 163 111 33 0.3 1 7 26 112 13 0.3 1 3 10 113 2 0.3 1 1 1 114 5 0.3 1 0 5 115 8 0.3 1 3 5 116 16 0.3 1 3 13 117 1 0.3 1 1 118 1 0.3 1 1 120 1 0.3 1 0 1 121 2 0.3 1 1 1 122 1 0.3 1 1 123 4 0.3 1 4 124 1 0.3 1 1 125 2 0.3 1 1 1 126 2 0.3 1 1 1 127 3 0.3 1 2 1 128 5 0.3 1 5 129 6 0.3 1 5 1 130 6 0.3 1 6 131 7 0.3 1 5 2 132 11 0.3 1 9 2 133 47 0.3 1 23 24 134 49 0.3 1 36 13 135 71 0.3 1 60 11 136 135 0.3 1 112 23 137 10902 0.3 1 10591 311 138 40576 0.3 1 39381 1195 139 3 0.3 1 0 3 140 7 0.3 1 1 6 143 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041630_val_1.fq.gz ============================================= 18184059 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1067879 (5.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 8065517 (44.4%)