SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041608_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/20201118/tmp/66177452-5592-11eb-8b6f-6c92bfc13046/trimmed/RRBS20A041608_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 917.09 s (25 us/read; 2.43 M reads/minute). === Summary === Total reads processed: 37,199,102 Reads with adapters: 15,536,681 (41.8%) Reads written (passing filters): 37,199,102 (100.0%) Total basepairs processed: 4,035,595,676 bp Total written (filtered): 4,005,873,640 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15536681 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 0.7% G: 20.3% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11456679 9299775.5 0 11456679 2 3010552 2324943.9 0 3010552 3 753017 581236.0 0 753017 4 165105 145309.0 0 165105 5 7128 36327.2 0 7128 6 3391 9081.8 0 3391 7 3091 2270.5 0 3091 8 1447 567.6 0 1447 9 2767 141.9 0 2272 495 10 4336 35.5 1 936 3400 11 2827 8.9 1 246 2581 12 1328 2.2 1 114 1214 13 1025 0.6 1 85 940 14 2410 0.6 1 181 2229 15 1501 0.6 1 129 1372 16 4480 0.6 1 372 4108 17 5029 0.6 1 428 4601 18 1855 0.6 1 196 1659 19 110 0.6 1 3 107 20 913 0.6 1 64 849 21 106 0.6 1 6 100 22 197 0.6 1 14 183 23 981 0.6 1 83 898 24 4093 0.6 1 370 3723 25 1606 0.6 1 152 1454 26 598 0.6 1 55 543 27 1444 0.6 1 150 1294 28 2945 0.6 1 254 2691 29 3358 0.6 1 312 3046 30 795 0.6 1 81 714 31 193 0.6 1 22 171 32 1210 0.6 1 99 1111 33 2559 0.6 1 208 2351 34 2902 0.6 1 264 2638 35 1226 0.6 1 97 1129 36 1101 0.6 1 98 1003 37 2323 0.6 1 190 2133 38 565 0.6 1 50 515 39 376 0.6 1 36 340 40 1630 0.6 1 126 1504 41 832 0.6 1 73 759 42 1434 0.6 1 116 1318 43 3006 0.6 1 273 2733 44 411 0.6 1 24 387 45 1226 0.6 1 93 1133 46 331 0.6 1 34 297 47 587 0.6 1 40 547 48 2054 0.6 1 182 1872 49 222 0.6 1 20 202 50 905 0.6 1 72 833 51 264 0.6 1 28 236 52 253 0.6 1 23 230 53 632 0.6 1 59 573 54 1884 0.6 1 175 1709 55 1485 0.6 1 121 1364 56 844 0.6 1 72 772 57 768 0.6 1 67 701 58 514 0.6 1 42 472 59 292 0.6 1 25 267 60 541 0.6 1 58 483 61 705 0.6 1 57 648 62 2228 0.6 1 235 1993 63 414 0.6 1 37 377 64 70 0.6 1 4 66 65 68 0.6 1 11 57 66 407 0.6 1 43 364 67 220 0.6 1 15 205 68 698 0.6 1 66 632 69 768 0.6 1 57 711 70 1359 0.6 1 101 1258 71 430 0.6 1 46 384 72 131 0.6 1 11 120 73 475 0.6 1 41 434 74 379 0.6 1 36 343 75 361 0.6 1 37 324 76 343 0.6 1 27 316 77 479 0.6 1 28 451 78 391 0.6 1 26 365 79 377 0.6 1 28 349 80 610 0.6 1 35 575 81 362 0.6 1 21 341 82 485 0.6 1 56 429 83 471 0.6 1 45 426 84 452 0.6 1 39 413 85 726 0.6 1 71 655 86 377 0.6 1 40 337 87 267 0.6 1 22 245 88 277 0.6 1 17 260 89 322 0.6 1 36 286 90 271 0.6 1 13 258 91 218 0.6 1 23 195 92 197 0.6 1 16 181 93 498 0.6 1 29 469 94 758 0.6 1 59 699 95 290 0.6 1 18 272 96 182 0.6 1 18 164 97 717 0.6 1 63 654 98 155 0.6 1 9 146 99 171 0.6 1 23 148 100 140 0.6 1 8 132 101 127 0.6 1 10 117 102 291 0.6 1 29 262 103 102 0.6 1 10 92 104 52 0.6 1 6 46 105 50 0.6 1 6 44 106 80 0.6 1 5 75 107 17 0.6 1 2 15 108 6 0.6 1 0 6 109 24 0.6 1 0 24 110 13 0.6 1 1 12 111 2 0.6 1 0 2 112 1 0.6 1 0 1 117 1 0.6 1 0 1 120 2 0.6 1 0 2 121 1 0.6 1 1 124 1 0.6 1 0 1 125 1 0.6 1 0 1 126 1 0.6 1 0 1 127 5 0.6 1 0 5 129 2 0.6 1 2 131 5 0.6 1 3 2 132 10 0.6 1 3 7 133 47 0.6 1 3 44 134 15 0.6 1 11 4 135 12 0.6 1 10 2 136 23 0.6 1 20 3 137 307 0.6 1 284 23 138 39544 0.6 1 38603 941 140 6 0.6 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041608_val_1.fq.gz ============================================= 37199102 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1534351 (4.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15536681 (41.8%)