SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041612_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/691b5038-5592-11eb-9756-6c92bfc12ef6/trimmed/RRBS20A041612_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 591.02 s (25 us/read; 2.40 M reads/minute). === Summary === Total reads processed: 23,619,066 Reads with adapters: 10,668,202 (45.2%) Reads written (passing filters): 23,619,066 (100.0%) Total basepairs processed: 2,603,628,373 bp Total written (filtered): 2,579,106,028 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10668202 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 2.6% G: 19.8% T: 46.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7627048 5904766.5 0 7627048 2 2076733 1476191.6 0 2076733 3 603461 369047.9 0 603461 4 125996 92262.0 0 125996 5 11931 23065.5 0 11931 6 12492 5766.4 0 12492 7 10544 1441.6 0 10544 8 10994 360.4 0 10994 9 12706 90.1 0 12078 628 10 15623 22.5 1 10828 4795 11 4733 5.6 1 937 3796 12 2526 1.4 1 473 2053 13 1911 0.4 1 312 1599 14 3324 0.4 1 545 2779 15 2627 0.4 1 490 2137 16 6397 0.4 1 1263 5134 17 6518 0.4 1 1099 5419 18 4412 0.4 1 956 3456 19 191 0.4 1 11 180 20 1871 0.4 1 379 1492 21 140 0.4 1 17 123 22 357 0.4 1 51 306 23 1910 0.4 1 353 1557 24 4859 0.4 1 873 3986 25 2452 0.4 1 459 1993 26 561 0.4 1 60 501 27 2646 0.4 1 489 2157 28 4393 0.4 1 861 3532 29 4321 0.4 1 830 3491 30 1929 0.4 1 470 1459 31 402 0.4 1 32 370 32 2875 0.4 1 575 2300 33 3766 0.4 1 711 3055 34 4334 0.4 1 786 3548 35 3089 0.4 1 600 2489 36 2107 0.4 1 361 1746 37 2902 0.4 1 535 2367 38 443 0.4 1 72 371 39 350 0.4 1 51 299 40 1574 0.4 1 251 1323 41 1227 0.4 1 219 1008 42 2138 0.4 1 377 1761 43 3340 0.4 1 599 2741 44 439 0.4 1 43 396 45 1888 0.4 1 374 1514 46 589 0.4 1 122 467 47 1208 0.4 1 189 1019 48 3208 0.4 1 634 2574 49 284 0.4 1 37 247 50 1218 0.4 1 209 1009 51 335 0.4 1 51 284 52 393 0.4 1 56 337 53 947 0.4 1 160 787 54 1924 0.4 1 303 1621 55 1879 0.4 1 321 1558 56 993 0.4 1 139 854 57 1092 0.4 1 177 915 58 697 0.4 1 111 586 59 259 0.4 1 33 226 60 547 0.4 1 84 463 61 740 0.4 1 116 624 62 1664 0.4 1 276 1388 63 446 0.4 1 87 359 64 56 0.4 1 10 46 65 40 0.4 1 4 36 66 225 0.4 1 41 184 67 214 0.4 1 27 187 68 848 0.4 1 129 719 69 968 0.4 1 153 815 70 1221 0.4 1 188 1033 71 344 0.4 1 45 299 72 132 0.4 1 14 118 73 429 0.4 1 52 377 74 384 0.4 1 59 325 75 424 0.4 1 72 352 76 442 0.4 1 77 365 77 464 0.4 1 89 375 78 374 0.4 1 67 307 79 415 0.4 1 64 351 80 487 0.4 1 68 419 81 361 0.4 1 54 307 82 410 0.4 1 63 347 83 430 0.4 1 52 378 84 395 0.4 1 50 345 85 441 0.4 1 80 361 86 330 0.4 1 41 289 87 279 0.4 1 37 242 88 294 0.4 1 33 261 89 298 0.4 1 49 249 90 230 0.4 1 28 202 91 196 0.4 1 22 174 92 215 0.4 1 29 186 93 421 0.4 1 53 368 94 402 0.4 1 53 349 95 226 0.4 1 32 194 96 151 0.4 1 19 132 97 341 0.4 1 36 305 98 103 0.4 1 14 89 99 97 0.4 1 10 87 100 91 0.4 1 14 77 101 78 0.4 1 8 70 102 116 0.4 1 22 94 103 69 0.4 1 13 56 104 40 0.4 1 6 34 105 25 0.4 1 2 23 106 31 0.4 1 6 25 107 15 0.4 1 4 11 108 7 0.4 1 1 6 109 16 0.4 1 1 15 110 8 0.4 1 1 7 111 4 0.4 1 1 3 112 2 0.4 1 1 1 113 1 0.4 1 1 114 1 0.4 1 0 1 115 4 0.4 1 1 3 116 3 0.4 1 0 3 117 3 0.4 1 0 3 118 2 0.4 1 1 1 119 1 0.4 1 1 121 1 0.4 1 0 1 122 1 0.4 1 1 123 1 0.4 1 1 124 1 0.4 1 1 126 1 0.4 1 0 1 127 7 0.4 1 0 7 128 6 0.4 1 1 5 129 1 0.4 1 1 130 3 0.4 1 1 2 131 4 0.4 1 1 3 132 10 0.4 1 3 7 133 26 0.4 1 7 19 134 24 0.4 1 18 6 135 17 0.4 1 15 2 136 17 0.4 1 14 3 137 323 0.4 1 295 28 138 39247 0.4 1 38314 933 140 5 0.4 1 0 5 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041612_val_1.fq.gz ============================================= 23619066 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1001503 (4.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10668201 (45.2%)