SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041599_val_2.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/20201110/tmp/cd5bec26-5581-11eb-aec1-6c92bfc12bba/trimmed/RRBS20A041599_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1161.10 s (43 us/read; 1.40 M reads/minute). === Summary === Total reads processed: 26,999,619 Reads with adapters: 9,633,289 (35.7%) Reads written (passing filters): 26,999,619 (100.0%) Total basepairs processed: 2,639,749,956 bp Total written (filtered): 2,613,374,414 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9633289 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.9% C: 75.0% G: 1.0% T: 7.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9422214 6749904.8 0 9422214 2 35996 1687476.2 0 35996 3 11718 421869.0 0 11718 4 8227 105467.3 0 8227 5 1499 26366.8 0 1499 6 934 6591.7 0 934 7 1573 1647.9 0 1573 8 1019 412.0 0 1019 9 705 103.0 0 683 22 10 2768 25.7 1 641 2127 11 301 6.4 1 48 253 12 605 1.6 1 73 532 13 675 0.4 1 78 597 14 1131 0.4 1 116 1015 15 354 0.4 1 36 318 16 456 0.4 1 62 394 17 817 0.4 1 95 722 18 266 0.4 1 22 244 19 1007 0.4 1 104 903 20 723 0.4 1 62 661 21 48 0.4 1 5 43 22 177 0.4 1 15 162 23 760 0.4 1 68 692 24 2283 0.4 1 214 2069 25 744 0.4 1 66 678 26 1149 0.4 1 113 1036 27 707 0.4 1 69 638 28 523 0.4 1 71 452 29 97 0.4 1 10 87 30 338 0.4 1 27 311 31 201 0.4 1 15 186 32 863 0.4 1 76 787 33 1196 0.4 1 122 1074 34 402 0.4 1 29 373 35 450 0.4 1 56 394 36 322 0.4 1 31 291 37 841 0.4 1 86 755 38 318 0.4 1 36 282 39 354 0.4 1 34 320 40 277 0.4 1 23 254 41 379 0.4 1 36 343 42 603 0.4 1 64 539 43 324 0.4 1 31 293 44 396 0.4 1 36 360 45 856 0.4 1 69 787 46 431 0.4 1 36 395 47 241 0.4 1 29 212 48 600 0.4 1 52 548 49 446 0.4 1 40 406 50 392 0.4 1 35 357 51 565 0.4 1 59 506 52 761 0.4 1 66 695 53 319 0.4 1 36 283 54 403 0.4 1 42 361 55 404 0.4 1 42 362 56 190 0.4 1 15 175 57 443 0.4 1 31 412 58 436 0.4 1 43 393 59 299 0.4 1 22 277 60 402 0.4 1 37 365 61 515 0.4 1 43 472 62 609 0.4 1 56 553 63 542 0.4 1 62 480 64 253 0.4 1 25 228 65 183 0.4 1 14 169 66 492 0.4 1 57 435 67 302 0.4 1 31 271 68 323 0.4 1 30 293 69 294 0.4 1 32 262 70 270 0.4 1 28 242 71 265 0.4 1 25 240 72 287 0.4 1 31 256 73 228 0.4 1 19 209 74 244 0.4 1 18 226 75 620 0.4 1 59 561 76 483 0.4 1 57 426 77 380 0.4 1 43 337 78 234 0.4 1 21 213 79 228 0.4 1 19 209 80 234 0.4 1 18 216 81 170 0.4 1 17 153 82 229 0.4 1 29 200 83 197 0.4 1 14 183 84 240 0.4 1 13 227 85 199 0.4 1 12 187 86 177 0.4 1 15 162 87 131 0.4 1 14 117 88 114 0.4 1 6 108 89 149 0.4 1 13 136 90 125 0.4 1 4 121 91 100 0.4 1 8 92 92 95 0.4 1 11 84 93 134 0.4 1 12 122 94 118 0.4 1 10 108 95 60 0.4 1 6 54 96 65 0.4 1 6 59 97 87 0.4 1 11 76 98 69 0.4 1 7 62 99 93 0.4 1 8 85 100 83 0.4 1 3 80 101 66 0.4 1 3 63 102 99 0.4 1 9 90 103 54 0.4 1 4 50 104 40 0.4 1 5 35 105 28 0.4 1 5 23 106 14 0.4 1 4 10 107 13 0.4 1 3 10 108 13 0.4 1 0 13 109 38 0.4 1 3 35 110 16 0.4 1 3 13 111 1 0.4 1 0 1 112 1 0.4 1 0 1 114 3 0.4 1 0 3 116 1 0.4 1 0 1 117 2 0.4 1 1 1 119 1 0.4 1 1 123 1 0.4 1 1 125 2 0.4 1 1 1 126 1 0.4 1 1 127 1 0.4 1 1 128 2 0.4 1 2 129 2 0.4 1 1 1 130 2 0.4 1 1 1 131 2 0.4 1 1 1 132 3 0.4 1 2 1 133 2 0.4 1 2 134 6 0.4 1 6 135 15 0.4 1 12 3 136 63 0.4 1 57 6 137 2836 0.4 1 2736 100 138 106412 0.4 1 104547 1865 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041599_val_2.fq.gz ============================================= 26999619 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1113780 (4.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 26999619 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 210757 (0.78%)