SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041686_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/caea572a-5581-11eb-b08d-6c92bfc13316/trimmed/RRBS20A041686_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1965.01 s (59 us/read; 1.02 M reads/minute). === Summary === Total reads processed: 33,457,696 Reads with adapters: 13,186,257 (39.4%) Reads written (passing filters): 33,457,696 (100.0%) Total basepairs processed: 3,326,353,540 bp Total written (filtered): 3,269,120,793 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13186257 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.3% C: 73.6% G: 0.5% T: 6.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12791417 8364424.0 0 12791417 2 31562 2091106.0 0 31562 3 3935 522776.5 0 3935 4 6597 130694.1 0 6597 5 2042 32673.5 0 2042 6 894 8168.4 0 894 7 1825 2042.1 0 1825 8 1481 510.5 0 1481 9 552 127.6 0 537 15 10 2207 31.9 1 450 1757 11 180 8.0 1 45 135 12 358 2.0 1 36 322 13 553 0.5 1 30 523 14 773 0.5 1 52 721 15 391 0.5 1 19 372 16 414 0.5 1 22 392 17 650 0.5 1 33 617 18 322 0.5 1 15 307 19 744 0.5 1 47 697 20 639 0.5 1 40 599 21 32 0.5 1 2 30 22 157 0.5 1 8 149 23 626 0.5 1 35 591 24 1853 0.5 1 86 1767 25 521 0.5 1 27 494 26 1350 0.5 1 56 1294 27 259 0.5 1 14 245 28 223 0.5 1 14 209 29 67 0.5 1 4 63 30 109 0.5 1 5 104 31 534 0.5 1 34 500 32 671 0.5 1 25 646 33 1766 0.5 1 79 1687 34 163 0.5 1 5 158 35 95 0.5 1 5 90 36 91 0.5 1 4 87 37 689 0.5 1 45 644 38 206 0.5 1 12 194 39 299 0.5 1 25 274 40 267 0.5 1 14 253 41 292 0.5 1 15 277 42 576 0.5 1 23 553 43 291 0.5 1 10 281 44 415 0.5 1 20 395 45 954 0.5 1 35 919 46 483 0.5 1 17 466 47 171 0.5 1 10 161 48 563 0.5 1 25 538 49 307 0.5 1 16 291 50 517 0.5 1 12 505 51 587 0.5 1 18 569 52 580 0.5 1 31 549 53 66 0.5 1 4 62 54 352 0.5 1 11 341 55 258 0.5 1 9 249 56 63 0.5 1 7 56 57 223 0.5 1 8 215 58 655 0.5 1 24 631 59 264 0.5 1 16 248 60 494 0.5 1 32 462 61 594 0.5 1 53 541 62 748 0.5 1 82 666 63 648 0.5 1 90 558 64 289 0.5 1 21 268 65 160 0.5 1 11 149 66 462 0.5 1 27 435 67 291 0.5 1 16 275 68 306 0.5 1 9 297 69 263 0.5 1 14 249 70 291 0.5 1 10 281 71 283 0.5 1 17 266 72 260 0.5 1 12 248 73 296 0.5 1 15 281 74 319 0.5 1 19 300 75 499 0.5 1 26 473 76 525 0.5 1 33 492 77 425 0.5 1 14 411 78 261 0.5 1 16 245 79 306 0.5 1 14 292 80 266 0.5 1 20 246 81 257 0.5 1 13 244 82 269 0.5 1 10 259 83 374 0.5 1 17 357 84 405 0.5 1 28 377 85 349 0.5 1 23 326 86 216 0.5 1 11 205 87 207 0.5 1 11 196 88 197 0.5 1 11 186 89 237 0.5 1 9 228 90 192 0.5 1 5 187 91 154 0.5 1 10 144 92 191 0.5 1 5 186 93 192 0.5 1 12 180 94 196 0.5 1 7 189 95 120 0.5 1 5 115 96 113 0.5 1 5 108 97 129 0.5 1 6 123 98 116 0.5 1 4 112 99 179 0.5 1 14 165 100 167 0.5 1 12 155 101 98 0.5 1 3 95 102 190 0.5 1 12 178 103 63 0.5 1 2 61 104 60 0.5 1 6 54 105 41 0.5 1 5 36 106 26 0.5 1 1 25 107 20 0.5 1 0 20 108 19 0.5 1 0 19 109 40 0.5 1 2 38 110 51 0.5 1 3 48 111 5 0.5 1 0 5 112 3 0.5 1 1 2 113 4 0.5 1 2 2 114 8 0.5 1 2 6 115 4 0.5 1 3 1 116 3 0.5 1 2 1 118 3 0.5 1 2 1 119 1 0.5 1 1 120 2 0.5 1 1 1 122 1 0.5 1 1 123 2 0.5 1 2 124 3 0.5 1 3 125 3 0.5 1 1 2 126 4 0.5 1 4 127 9 0.5 1 9 128 9 0.5 1 9 129 13 0.5 1 11 2 130 14 0.5 1 11 3 131 15 0.5 1 13 2 132 6 0.5 1 4 2 133 27 0.5 1 23 4 134 31 0.5 1 30 1 135 64 0.5 1 58 6 136 180 0.5 1 167 13 137 8005 0.5 1 7842 163 138 299853 0.5 1 295594 4259 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041686_val_2.fq.gz ============================================= 33457696 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1507934 (4.5%) 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: 33457696 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 402729 (1.20%)