SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041590_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/68c6048e-5592-11eb-8c03-6c92bfc12ff2/trimmed/RRBS20A041590_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 104.06 s (24 us/read; 2.49 M reads/minute). === Summary === Total reads processed: 4,322,205 Reads with adapters: 1,794,356 (41.5%) Reads written (passing filters): 4,322,205 (100.0%) Total basepairs processed: 475,067,979 bp Total written (filtered): 470,842,318 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1794356 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.0% C: 0.8% G: 22.6% T: 49.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1287624 1080551.2 0 1287624 2 362272 270137.8 0 362272 3 93962 67534.5 0 93962 4 19354 16883.6 0 19354 5 1210 4220.9 0 1210 6 805 1055.2 0 805 7 644 263.8 0 644 8 548 66.0 0 548 9 821 16.5 0 754 67 10 826 4.1 1 340 486 11 493 1.0 1 96 397 12 265 0.3 1 44 221 13 260 0.1 1 51 209 14 465 0.1 1 79 386 15 359 0.1 1 81 278 16 978 0.1 1 172 806 17 1186 0.1 1 225 961 18 468 0.1 1 124 344 19 18 0.1 1 1 17 20 197 0.1 1 38 159 21 18 0.1 1 6 12 22 43 0.1 1 8 35 23 207 0.1 1 34 173 24 663 0.1 1 145 518 25 307 0.1 1 58 249 26 98 0.1 1 17 81 27 309 0.1 1 55 254 28 637 0.1 1 128 509 29 610 0.1 1 134 476 30 186 0.1 1 38 148 31 41 0.1 1 4 37 32 299 0.1 1 57 242 33 480 0.1 1 78 402 34 499 0.1 1 111 388 35 277 0.1 1 44 233 36 252 0.1 1 35 217 37 432 0.1 1 86 346 38 98 0.1 1 20 78 39 73 0.1 1 14 59 40 320 0.1 1 60 260 41 297 0.1 1 53 244 42 357 0.1 1 77 280 43 591 0.1 1 139 452 44 89 0.1 1 7 82 45 256 0.1 1 46 210 46 86 0.1 1 10 76 47 158 0.1 1 19 139 48 524 0.1 1 118 406 49 32 0.1 1 3 29 50 210 0.1 1 31 179 51 65 0.1 1 12 53 52 47 0.1 1 6 41 53 127 0.1 1 21 106 54 429 0.1 1 94 335 55 312 0.1 1 60 252 56 156 0.1 1 34 122 57 215 0.1 1 49 166 58 109 0.1 1 18 91 59 57 0.1 1 10 47 60 103 0.1 1 24 79 61 138 0.1 1 28 110 62 359 0.1 1 75 284 63 75 0.1 1 16 59 64 15 0.1 1 4 11 65 9 0.1 1 2 7 66 59 0.1 1 10 49 67 40 0.1 1 8 32 68 186 0.1 1 38 148 69 158 0.1 1 35 123 70 312 0.1 1 62 250 71 83 0.1 1 20 63 72 24 0.1 1 6 18 73 84 0.1 1 18 66 74 69 0.1 1 17 52 75 71 0.1 1 15 56 76 94 0.1 1 20 74 77 98 0.1 1 18 80 78 99 0.1 1 23 76 79 79 0.1 1 18 61 80 169 0.1 1 36 133 81 87 0.1 1 21 66 82 90 0.1 1 27 63 83 94 0.1 1 19 75 84 79 0.1 1 10 69 85 96 0.1 1 23 73 86 70 0.1 1 16 54 87 54 0.1 1 10 44 88 57 0.1 1 8 49 89 48 0.1 1 8 40 90 43 0.1 1 11 32 91 53 0.1 1 12 41 92 54 0.1 1 13 41 93 122 0.1 1 26 96 94 189 0.1 1 32 157 95 80 0.1 1 15 65 96 65 0.1 1 13 52 97 219 0.1 1 51 168 98 37 0.1 1 7 30 99 23 0.1 1 4 19 100 28 0.1 1 6 22 101 21 0.1 1 5 16 102 47 0.1 1 9 38 103 14 0.1 1 6 8 104 5 0.1 1 1 4 105 6 0.1 1 1 5 106 5 0.1 1 3 2 107 2 0.1 1 1 1 108 2 0.1 1 1 1 110 3 0.1 1 2 1 131 1 0.1 1 1 133 4 0.1 1 1 3 134 5 0.1 1 3 2 135 2 0.1 1 1 1 136 6 0.1 1 6 137 227 0.1 1 219 8 138 7373 0.1 1 7166 207 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041590_val_1.fq.gz ============================================= 4322205 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 170754 (4.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 1794356 (41.5%)