SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041607_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/20201120/tmp/a700d9c4-5572-11eb-ad2c-6c92bfc3978c/trimmed/RRBS20A041607_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 483.65 s (23 us/read; 2.61 M reads/minute). === Summary === Total reads processed: 21,011,298 Reads with adapters: 7,859,830 (37.4%) Reads written (passing filters): 21,011,298 (100.0%) Total basepairs processed: 2,114,891,785 bp Total written (filtered): 2,032,675,032 bp (96.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7859830 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.6% C: 77.2% G: 0.6% T: 5.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7244962 5252824.5 0 7244962 2 36831 1313206.1 0 36831 3 4858 328301.5 0 4858 4 6769 82075.4 0 6769 5 1984 20518.8 0 1984 6 791 5129.7 0 791 7 1140 1282.4 0 1140 8 1017 320.6 0 1017 9 328 80.2 0 314 14 10 1555 20.0 1 246 1309 11 126 5.0 1 15 111 12 334 1.3 1 19 315 13 469 0.3 1 24 445 14 516 0.3 1 36 480 15 255 0.3 1 11 244 16 364 0.3 1 20 344 17 498 0.3 1 29 469 18 255 0.3 1 14 241 19 547 0.3 1 30 517 20 543 0.3 1 28 515 21 33 0.3 1 1 32 22 107 0.3 1 5 102 23 429 0.3 1 27 402 24 1098 0.3 1 57 1041 25 448 0.3 1 16 432 26 1020 0.3 1 45 975 27 221 0.3 1 16 205 28 248 0.3 1 19 229 29 66 0.3 1 2 64 30 105 0.3 1 9 96 31 393 0.3 1 30 363 32 441 0.3 1 24 417 33 1256 0.3 1 62 1194 34 104 0.3 1 4 100 35 83 0.3 1 5 78 36 59 0.3 1 2 57 37 458 0.3 1 22 436 38 192 0.3 1 14 178 39 271 0.3 1 24 247 40 251 0.3 1 13 238 41 281 0.3 1 13 268 42 376 0.3 1 19 357 43 249 0.3 1 11 238 44 295 0.3 1 15 280 45 561 0.3 1 29 532 46 371 0.3 1 13 358 47 183 0.3 1 8 175 48 374 0.3 1 21 353 49 281 0.3 1 16 265 50 529 0.3 1 16 513 51 528 0.3 1 36 492 52 492 0.3 1 36 456 53 84 0.3 1 4 80 54 304 0.3 1 9 295 55 322 0.3 1 22 300 56 72 0.3 1 4 68 57 229 0.3 1 7 222 58 536 0.3 1 33 503 59 235 0.3 1 18 217 60 329 0.3 1 22 307 61 405 0.3 1 48 357 62 573 0.3 1 113 460 63 559 0.3 1 104 455 64 246 0.3 1 25 221 65 155 0.3 1 16 139 66 556 0.3 1 32 524 67 264 0.3 1 18 246 68 211 0.3 1 10 201 69 224 0.3 1 11 213 70 226 0.3 1 12 214 71 199 0.3 1 10 189 72 229 0.3 1 19 210 73 196 0.3 1 11 185 74 248 0.3 1 12 236 75 424 0.3 1 30 394 76 420 0.3 1 28 392 77 277 0.3 1 10 267 78 189 0.3 1 4 185 79 198 0.3 1 9 189 80 181 0.3 1 9 172 81 191 0.3 1 3 188 82 196 0.3 1 10 186 83 247 0.3 1 6 241 84 266 0.3 1 7 259 85 245 0.3 1 16 229 86 136 0.3 1 4 132 87 119 0.3 1 7 112 88 123 0.3 1 9 114 89 140 0.3 1 5 135 90 110 0.3 1 5 105 91 90 0.3 1 7 83 92 92 0.3 1 3 89 93 118 0.3 1 5 113 94 123 0.3 1 10 113 95 77 0.3 1 5 72 96 66 0.3 1 4 62 97 85 0.3 1 4 81 98 71 0.3 1 3 68 99 99 0.3 1 7 92 100 92 0.3 1 2 90 101 64 0.3 1 1 63 102 110 0.3 1 8 102 103 46 0.3 1 3 43 104 23 0.3 1 2 21 105 21 0.3 1 4 17 106 19 0.3 1 1 18 107 14 0.3 1 1 13 108 8 0.3 1 1 7 109 28 0.3 1 3 25 110 21 0.3 1 1 20 111 2 0.3 1 1 1 112 2 0.3 1 0 2 113 4 0.3 1 3 1 114 3 0.3 1 0 3 115 1 0.3 1 1 116 4 0.3 1 4 117 5 0.3 1 5 118 4 0.3 1 3 1 119 2 0.3 1 2 120 6 0.3 1 6 121 1 0.3 1 0 1 122 1 0.3 1 0 1 123 6 0.3 1 6 124 1 0.3 1 0 1 125 2 0.3 1 2 126 3 0.3 1 3 127 9 0.3 1 9 128 29 0.3 1 27 2 129 22 0.3 1 21 1 130 11 0.3 1 11 131 19 0.3 1 17 2 132 26 0.3 1 22 4 133 37 0.3 1 35 2 134 52 0.3 1 45 7 135 150 0.3 1 135 15 136 378 0.3 1 357 21 137 9832 0.3 1 9617 215 138 522142 0.3 1 515027 7115 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041607_val_2.fq.gz ============================================= 21011298 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1101883 (5.2%) 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: 21011298 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 593666 (2.83%)