SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041585_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/caf4347a-5581-11eb-a01e-6c92bfc13316/trimmed/RRBS20A041585_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 979.81 s (36 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 27,551,916 Reads with adapters: 10,866,475 (39.4%) Reads written (passing filters): 27,551,916 (100.0%) Total basepairs processed: 2,768,587,638 bp Total written (filtered): 2,680,315,148 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10866475 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.5% C: 68.7% G: 6.4% T: 6.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10156306 6887979.0 0 10156306 2 95699 1721994.8 0 95699 3 11798 430498.7 0 11798 4 4898 107624.7 0 4898 5 1317 26906.2 0 1317 6 726 6726.5 0 726 7 1553 1681.6 0 1553 8 738 420.4 0 738 9 341 105.1 0 306 35 10 3644 26.3 1 863 2781 11 143 6.6 1 26 117 12 2905 1.6 1 568 2337 13 929 0.4 1 125 804 14 968 0.4 1 61 907 15 291 0.4 1 18 273 16 337 0.4 1 19 318 17 706 0.4 1 72 634 18 286 0.4 1 11 275 19 808 0.4 1 49 759 20 558 0.4 1 35 523 21 67 0.4 1 21 46 22 427 0.4 1 30 397 23 592 0.4 1 31 561 24 1827 0.4 1 122 1705 25 553 0.4 1 25 528 26 899 0.4 1 52 847 27 276 0.4 1 16 260 28 516 0.4 1 31 485 29 63 0.4 1 1 62 30 546 0.4 1 33 513 31 453 0.4 1 22 431 32 613 0.4 1 36 577 33 1201 0.4 1 79 1122 34 369 0.4 1 34 335 35 572 0.4 1 36 536 36 221 0.4 1 9 212 37 691 0.4 1 51 640 38 217 0.4 1 15 202 39 257 0.4 1 12 245 40 183 0.4 1 11 172 41 585 0.4 1 20 565 42 752 0.4 1 37 715 43 220 0.4 1 13 207 44 331 0.4 1 16 315 45 928 0.4 1 67 861 46 354 0.4 1 27 327 47 164 0.4 1 8 156 48 663 0.4 1 64 599 49 328 0.4 1 16 312 50 366 0.4 1 31 335 51 627 0.4 1 50 577 52 753 0.4 1 62 691 53 313 0.4 1 22 291 54 394 0.4 1 27 367 55 298 0.4 1 19 279 56 171 0.4 1 11 160 57 354 0.4 1 25 329 58 424 0.4 1 23 401 59 280 0.4 1 26 254 60 373 0.4 1 51 322 61 489 0.4 1 92 397 62 650 0.4 1 143 507 63 524 0.4 1 94 430 64 264 0.4 1 33 231 65 211 0.4 1 22 189 66 525 0.4 1 66 459 67 308 0.4 1 34 274 68 282 0.4 1 27 255 69 235 0.4 1 15 220 70 249 0.4 1 19 230 71 234 0.4 1 23 211 72 259 0.4 1 17 242 73 228 0.4 1 16 212 74 226 0.4 1 22 204 75 493 0.4 1 25 468 76 564 0.4 1 36 528 77 363 0.4 1 23 340 78 229 0.4 1 12 217 79 241 0.4 1 16 225 80 243 0.4 1 14 229 81 166 0.4 1 11 155 82 201 0.4 1 15 186 83 207 0.4 1 19 188 84 286 0.4 1 31 255 85 236 0.4 1 17 219 86 161 0.4 1 19 142 87 132 0.4 1 10 122 88 131 0.4 1 11 120 89 125 0.4 1 8 117 90 112 0.4 1 11 101 91 98 0.4 1 10 88 92 103 0.4 1 10 93 93 132 0.4 1 12 120 94 127 0.4 1 9 118 95 73 0.4 1 3 70 96 89 0.4 1 7 82 97 82 0.4 1 7 75 98 59 0.4 1 4 55 99 110 0.4 1 10 100 100 80 0.4 1 6 74 101 48 0.4 1 4 44 102 112 0.4 1 11 101 103 48 0.4 1 6 42 104 37 0.4 1 3 34 105 31 0.4 1 6 25 106 17 0.4 1 4 13 107 11 0.4 1 3 8 108 22 0.4 1 1 21 109 18 0.4 1 1 17 110 30 0.4 1 1 29 111 7 0.4 1 3 4 112 1 0.4 1 1 113 3 0.4 1 1 2 114 3 0.4 1 1 2 115 6 0.4 1 3 3 116 4 0.4 1 2 2 117 2 0.4 1 1 1 118 8 0.4 1 4 4 119 2 0.4 1 2 120 3 0.4 1 3 121 2 0.4 1 1 1 122 1 0.4 1 1 123 2 0.4 1 1 1 124 8 0.4 1 5 3 125 6 0.4 1 6 126 5 0.4 1 5 127 26 0.4 1 23 3 128 28 0.4 1 23 5 129 39 0.4 1 34 5 130 25 0.4 1 25 131 36 0.4 1 31 5 132 33 0.4 1 27 6 133 62 0.4 1 57 5 134 61 0.4 1 57 4 135 189 0.4 1 173 16 136 635 0.4 1 590 45 137 33453 0.4 1 32726 727 138 517752 0.4 1 508886 8866 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041585_val_2.fq.gz ============================================= 27551916 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1050215 (3.8%) 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: 27551916 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 640452 (2.32%)