SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041591_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/a594373e-5572-11eb-9e34-6c92bfc12f32/trimmed/RRBS20A041591_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 484.40 s (22 us/read; 2.68 M reads/minute). === Summary === Total reads processed: 21,663,739 Reads with adapters: 9,377,154 (43.3%) Reads written (passing filters): 21,663,739 (100.0%) Total basepairs processed: 2,263,560,259 bp Total written (filtered): 2,210,821,633 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9377154 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.8% C: 0.6% G: 23.0% T: 45.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6720720 5415934.8 0 6720720 2 1715448 1353983.7 0 1715448 3 465762 338495.9 0 465762 4 101276 84624.0 0 101276 5 5816 21156.0 0 5816 6 3839 5289.0 0 3839 7 3354 1322.2 0 3354 8 2654 330.6 0 2654 9 3704 82.6 0 3377 327 10 4024 20.7 1 2157 1867 11 2543 5.2 1 359 2184 12 972 1.3 1 157 815 13 941 0.3 1 128 813 14 1484 0.3 1 177 1307 15 1026 0.3 1 134 892 16 3191 0.3 1 410 2781 17 4340 0.3 1 1044 3296 18 3263 0.3 1 1717 1546 19 114 0.3 1 14 100 20 892 0.3 1 151 741 21 111 0.3 1 15 96 22 178 0.3 1 22 156 23 857 0.3 1 106 751 24 2542 0.3 1 447 2095 25 989 0.3 1 144 845 26 391 0.3 1 61 330 27 1019 0.3 1 153 866 28 2312 0.3 1 410 1902 29 2305 0.3 1 310 1995 30 526 0.3 1 84 442 31 86 0.3 1 8 78 32 907 0.3 1 135 772 33 1541 0.3 1 232 1309 34 1331 0.3 1 210 1121 35 2340 0.3 1 354 1986 36 910 0.3 1 129 781 37 467 0.3 1 74 393 38 1789 0.3 1 335 1454 39 687 0.3 1 104 583 40 2189 0.3 1 303 1886 41 1458 0.3 1 195 1263 42 1361 0.3 1 207 1154 43 2674 0.3 1 359 2315 44 369 0.3 1 51 318 45 1143 0.3 1 162 981 46 379 0.3 1 54 325 47 762 0.3 1 93 669 48 2308 0.3 1 351 1957 49 249 0.3 1 23 226 50 1202 0.3 1 162 1040 51 416 0.3 1 42 374 52 241 0.3 1 24 217 53 720 0.3 1 83 637 54 2367 0.3 1 357 2010 55 1130 0.3 1 139 991 56 838 0.3 1 102 736 57 869 0.3 1 161 708 58 550 0.3 1 66 484 59 337 0.3 1 39 298 60 500 0.3 1 64 436 61 691 0.3 1 62 629 62 1814 0.3 1 245 1569 63 552 0.3 1 74 478 64 66 0.3 1 3 63 65 54 0.3 1 4 50 66 216 0.3 1 29 187 67 279 0.3 1 34 245 68 916 0.3 1 144 772 69 921 0.3 1 135 786 70 1833 0.3 1 256 1577 71 975 0.3 1 125 850 72 403 0.3 1 50 353 73 267 0.3 1 39 228 74 356 0.3 1 57 299 75 470 0.3 1 67 403 76 449 0.3 1 61 388 77 590 0.3 1 71 519 78 525 0.3 1 61 464 79 501 0.3 1 68 433 80 477 0.3 1 60 417 81 419 0.3 1 61 358 82 535 0.3 1 77 458 83 591 0.3 1 88 503 84 457 0.3 1 52 405 85 715 0.3 1 130 585 86 410 0.3 1 64 346 87 321 0.3 1 47 274 88 260 0.3 1 32 228 89 314 0.3 1 46 268 90 293 0.3 1 35 258 91 180 0.3 1 23 157 92 237 0.3 1 39 198 93 375 0.3 1 55 320 94 499 0.3 1 55 444 95 228 0.3 1 24 204 96 188 0.3 1 30 158 97 288 0.3 1 38 250 98 147 0.3 1 23 124 99 123 0.3 1 12 111 100 94 0.3 1 11 83 101 102 0.3 1 16 86 102 129 0.3 1 20 109 103 68 0.3 1 11 57 104 53 0.3 1 1 52 105 36 0.3 1 7 29 106 36 0.3 1 5 31 107 18 0.3 1 5 13 108 8 0.3 1 1 7 109 10 0.3 1 0 10 110 7 0.3 1 1 6 111 1 0.3 1 0 1 112 2 0.3 1 0 2 113 1 0.3 1 0 1 114 2 0.3 1 1 1 115 6 0.3 1 3 3 116 4 0.3 1 2 2 117 4 0.3 1 0 4 118 1 0.3 1 1 119 2 0.3 1 1 1 120 3 0.3 1 2 1 121 1 0.3 1 1 122 1 0.3 1 1 123 5 0.3 1 5 124 2 0.3 1 0 2 125 3 0.3 1 2 1 126 4 0.3 1 3 1 127 12 0.3 1 8 4 128 6 0.3 1 5 1 129 9 0.3 1 8 1 130 9 0.3 1 6 3 131 15 0.3 1 12 3 132 13 0.3 1 10 3 133 43 0.3 1 25 18 134 52 0.3 1 42 10 135 93 0.3 1 82 11 136 114 0.3 1 99 15 137 4431 0.3 1 4243 188 138 264096 0.3 1 257000 7096 140 10 0.3 1 0 10 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041591_val_1.fq.gz ============================================= 21663739 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 651161 (3.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 9377152 (43.3%)