SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041690_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/20201121/tmp/c309dc1a-3f65-11eb-a3a2-6c92bfc12bba/trimmed/RRBS20A041690_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 241.87 s (20 us/read; 3.02 M reads/minute). === Summary === Total reads processed: 12,178,016 Reads with adapters: 5,984,851 (49.1%) Reads written (passing filters): 12,178,016 (100.0%) Total basepairs processed: 1,267,759,940 bp Total written (filtered): 1,053,744,592 bp (83.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5984851 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.3% C: 26.1% G: 14.1% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3308541 3044504.0 0 3308541 2 868578 761126.0 0 868578 3 204834 190281.5 0 204834 4 46135 47570.4 0 46135 5 2275 11892.6 0 2275 6 1310 2973.1 0 1310 7 822 743.3 0 822 8 844 185.8 0 844 9 1331 46.5 0 1215 116 10 1111 11.6 1 440 671 11 1287 2.9 1 228 1059 12 404 0.7 1 60 344 13 491 0.2 1 87 404 14 824 0.2 1 164 660 15 806 0.2 1 160 646 16 1724 0.2 1 338 1386 17 3019 0.2 1 886 2133 18 3674 0.2 1 2600 1074 19 84 0.2 1 27 57 20 512 0.2 1 110 402 21 44 0.2 1 7 37 22 113 0.2 1 49 64 23 381 0.2 1 69 312 24 1362 0.2 1 261 1101 25 719 0.2 1 170 549 26 206 0.2 1 43 163 27 646 0.2 1 108 538 28 1377 0.2 1 324 1053 29 1346 0.2 1 293 1053 30 266 0.2 1 55 211 31 70 0.2 1 15 55 32 508 0.2 1 100 408 33 732 0.2 1 167 565 34 811 0.2 1 158 653 35 1578 0.2 1 335 1243 36 622 0.2 1 135 487 37 234 0.2 1 38 196 38 1039 0.2 1 187 852 39 362 0.2 1 69 293 40 1524 0.2 1 264 1260 41 1002 0.2 1 185 817 42 972 0.2 1 202 770 43 1991 0.2 1 376 1615 44 277 0.2 1 51 226 45 1004 0.2 1 200 804 46 232 0.2 1 35 197 47 538 0.2 1 89 449 48 1947 0.2 1 395 1552 49 148 0.2 1 21 127 50 742 0.2 1 152 590 51 288 0.2 1 56 232 52 178 0.2 1 38 140 53 521 0.2 1 110 411 54 2003 0.2 1 412 1591 55 980 0.2 1 190 790 56 396 0.2 1 65 331 57 858 0.2 1 177 681 58 360 0.2 1 62 298 59 178 0.2 1 36 142 60 420 0.2 1 74 346 61 458 0.2 1 61 397 62 1359 0.2 1 287 1072 63 442 0.2 1 83 359 64 54 0.2 1 8 46 65 38 0.2 1 6 32 66 164 0.2 1 33 131 67 192 0.2 1 27 165 68 690 0.2 1 122 568 69 811 0.2 1 165 646 70 1404 0.2 1 268 1136 71 629 0.2 1 102 527 72 265 0.2 1 43 222 73 219 0.2 1 34 185 74 289 0.2 1 63 226 75 412 0.2 1 98 314 76 445 0.2 1 98 347 77 515 0.2 1 95 420 78 476 0.2 1 100 376 79 444 0.2 1 115 329 80 563 0.2 1 100 463 81 422 0.2 1 77 345 82 585 0.2 1 119 466 83 595 0.2 1 108 487 84 569 0.2 1 115 454 85 620 0.2 1 135 485 86 478 0.2 1 114 364 87 300 0.2 1 46 254 88 283 0.2 1 57 226 89 313 0.2 1 61 252 90 275 0.2 1 63 212 91 246 0.2 1 44 202 92 273 0.2 1 59 214 93 701 0.2 1 102 599 94 1641 0.2 1 237 1404 95 477 0.2 1 68 409 96 293 0.2 1 60 233 97 1623 0.2 1 212 1411 98 210 0.2 1 45 165 99 135 0.2 1 21 114 100 167 0.2 1 34 133 101 168 0.2 1 30 138 102 337 0.2 1 80 257 103 121 0.2 1 26 95 104 89 0.2 1 28 61 105 50 0.2 1 11 39 106 48 0.2 1 13 35 107 25 0.2 1 4 21 108 11 0.2 1 3 8 109 20 0.2 1 3 17 110 31 0.2 1 6 25 111 9 0.2 1 3 6 112 7 0.2 1 5 2 113 7 0.2 1 2 5 114 59 0.2 1 9 50 115 7 0.2 1 7 116 4 0.2 1 1 3 117 8 0.2 1 6 2 118 4 0.2 1 3 1 119 6 0.2 1 6 120 7 0.2 1 5 2 121 2 0.2 1 1 1 122 10 0.2 1 8 2 123 7 0.2 1 4 3 124 16 0.2 1 14 2 125 8 0.2 1 6 2 126 8 0.2 1 6 2 127 17 0.2 1 12 5 128 29 0.2 1 25 4 129 53 0.2 1 40 13 130 54 0.2 1 44 10 131 63 0.2 1 53 10 132 90 0.2 1 67 23 133 231 0.2 1 189 42 134 351 0.2 1 296 55 135 455 0.2 1 385 70 136 907 0.2 1 815 92 137 81062 0.2 1 78798 2264 138 1402778 0.2 1 1373313 29465 139 10 0.2 1 6 4 140 21 0.2 1 11 10 141 4 0.2 1 1 3 143 1 0.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041690_val_1.fq.gz ============================================= 12178016 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 412229 (3.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 5984846 (49.1%)