SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041624_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/c364d976-3f65-11eb-8174-b4055d0383c6/trimmed/RRBS20A041624_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 220.94 s (23 us/read; 2.57 M reads/minute). === Summary === Total reads processed: 9,468,826 Reads with adapters: 3,846,196 (40.6%) Reads written (passing filters): 9,468,826 (100.0%) Total basepairs processed: 920,253,707 bp Total written (filtered): 897,347,078 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3846196 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.9% C: 1.0% G: 19.9% T: 46.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2696807 2367206.5 0 2696807 2 775215 591801.6 0 775215 3 179448 147950.4 0 179448 4 40101 36987.6 0 40101 5 2541 9246.9 0 2541 6 1290 2311.7 0 1290 7 797 577.9 0 797 8 813 144.5 0 813 9 843 36.1 0 734 109 10 1249 9.0 1 485 764 11 609 2.3 1 83 526 12 297 0.6 1 37 260 13 283 0.1 1 35 248 14 461 0.1 1 53 408 15 495 0.1 1 66 429 16 744 0.1 1 86 658 17 1187 0.1 1 148 1039 18 651 0.1 1 126 525 19 27 0.1 1 3 24 20 281 0.1 1 47 234 21 23 0.1 1 3 20 22 38 0.1 1 8 30 23 280 0.1 1 36 244 24 566 0.1 1 74 492 25 372 0.1 1 65 307 26 85 0.1 1 10 75 27 438 0.1 1 64 374 28 671 0.1 1 95 576 29 653 0.1 1 87 566 30 193 0.1 1 39 154 31 33 0.1 1 1 32 32 325 0.1 1 49 276 33 464 0.1 1 57 407 34 452 0.1 1 63 389 35 635 0.1 1 81 554 36 349 0.1 1 45 304 37 178 0.1 1 23 155 38 398 0.1 1 56 342 39 245 0.1 1 27 218 40 592 0.1 1 67 525 41 509 0.1 1 58 451 42 425 0.1 1 40 385 43 680 0.1 1 81 599 44 104 0.1 1 11 93 45 403 0.1 1 46 357 46 187 0.1 1 24 163 47 328 0.1 1 45 283 48 736 0.1 1 107 629 49 89 0.1 1 9 80 50 282 0.1 1 36 246 51 94 0.1 1 16 78 52 109 0.1 1 15 94 53 261 0.1 1 24 237 54 605 0.1 1 66 539 55 473 0.1 1 49 424 56 235 0.1 1 29 206 57 342 0.1 1 31 311 58 236 0.1 1 20 216 59 88 0.1 1 8 80 60 198 0.1 1 22 176 61 309 0.1 1 50 259 62 713 0.1 1 104 609 63 177 0.1 1 24 153 64 26 0.1 1 3 23 65 28 0.1 1 4 24 66 152 0.1 1 24 128 67 112 0.1 1 13 99 68 326 0.1 1 44 282 69 344 0.1 1 43 301 70 544 0.1 1 52 492 71 211 0.1 1 26 185 72 147 0.1 1 11 136 73 146 0.1 1 12 134 74 141 0.1 1 19 122 75 150 0.1 1 23 127 76 174 0.1 1 21 153 77 197 0.1 1 24 173 78 181 0.1 1 23 158 79 172 0.1 1 20 152 80 169 0.1 1 24 145 81 152 0.1 1 17 135 82 183 0.1 1 12 171 83 186 0.1 1 23 163 84 151 0.1 1 13 138 85 148 0.1 1 13 135 86 209 0.1 1 20 189 87 100 0.1 1 5 95 88 98 0.1 1 8 90 89 127 0.1 1 13 114 90 95 0.1 1 5 90 91 84 0.1 1 10 74 92 98 0.1 1 14 84 93 307 0.1 1 25 282 94 342 0.1 1 37 305 95 72 0.1 1 6 66 96 96 0.1 1 7 89 97 361 0.1 1 23 338 98 67 0.1 1 2 65 99 33 0.1 1 5 28 100 35 0.1 1 3 32 101 44 0.1 1 7 37 102 76 0.1 1 6 70 103 26 0.1 1 2 24 104 24 0.1 1 3 21 105 23 0.1 1 4 19 106 26 0.1 1 4 22 107 9 0.1 1 2 7 108 7 0.1 1 1 6 109 2 0.1 1 1 1 110 10 0.1 1 0 10 111 3 0.1 1 2 1 115 2 0.1 1 0 2 117 1 0.1 1 0 1 118 1 0.1 1 1 119 1 0.1 1 1 122 1 0.1 1 1 123 3 0.1 1 1 2 124 2 0.1 1 1 1 125 1 0.1 1 1 126 2 0.1 1 1 1 127 1 0.1 1 0 1 128 5 0.1 1 2 3 129 4 0.1 1 3 1 130 5 0.1 1 3 2 131 11 0.1 1 8 3 132 13 0.1 1 8 5 133 56 0.1 1 44 12 134 50 0.1 1 38 12 135 73 0.1 1 59 14 136 215 0.1 1 184 31 137 13987 0.1 1 13427 560 138 103741 0.1 1 99618 4123 139 37 0.1 1 32 5 140 2849 0.1 1 2636 213 142 1 0.1 1 1 143 8 0.1 1 4 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041624_val_1.fq.gz ============================================= 9468826 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 433363 (4.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 3846173 (40.6%)