SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041601_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/raw_data/cup/BS_workflow/20201121/tmp/c2f0e4d0-3f65-11eb-a7de-6c92bfc12c92/trimmed/RRBS20A041601_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 369.73 s (27 us/read; 2.21 M reads/minute). === Summary === Total reads processed: 13,633,322 Reads with adapters: 6,770,737 (49.7%) Reads written (passing filters): 13,633,322 (100.0%) Total basepairs processed: 1,406,060,421 bp Total written (filtered): 1,113,734,625 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6770737 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 11.8% C: 52.2% G: 32.0% T: 4.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4611111 3408330.5 0 4611111 2 41100 852082.6 0 41100 3 6232 213020.7 0 6232 4 3709 53255.2 0 3709 5 1303 13313.8 0 1303 6 541 3328.4 0 541 7 927 832.1 0 927 8 468 208.0 0 468 9 230 52.0 0 207 23 10 1997 13.0 1 443 1554 11 90 3.3 1 11 79 12 1562 0.8 1 379 1183 13 387 0.2 1 43 344 14 634 0.2 1 80 554 15 205 0.2 1 16 189 16 256 0.2 1 26 230 17 487 0.2 1 47 440 18 210 0.2 1 16 194 19 519 0.2 1 59 460 20 405 0.2 1 54 351 21 97 0.2 1 63 34 22 353 0.2 1 37 316 23 455 0.2 1 60 395 24 1129 0.2 1 116 1013 25 376 0.2 1 45 331 26 563 0.2 1 66 497 27 235 0.2 1 40 195 28 522 0.2 1 52 470 29 50 0.2 1 7 43 30 395 0.2 1 42 353 31 355 0.2 1 31 324 32 411 0.2 1 33 378 33 913 0.2 1 102 811 34 322 0.2 1 34 288 35 473 0.2 1 39 434 36 87 0.2 1 10 77 37 479 0.2 1 58 421 38 167 0.2 1 20 147 39 207 0.2 1 28 179 40 246 0.2 1 25 221 41 506 0.2 1 30 476 42 482 0.2 1 30 452 43 258 0.2 1 23 235 44 297 0.2 1 18 279 45 500 0.2 1 52 448 46 275 0.2 1 28 247 47 110 0.2 1 12 98 48 354 0.2 1 38 316 49 259 0.2 1 31 228 50 458 0.2 1 70 388 51 401 0.2 1 53 348 52 359 0.2 1 38 321 53 69 0.2 1 9 60 54 283 0.2 1 33 250 55 189 0.2 1 23 166 56 51 0.2 1 5 46 57 190 0.2 1 20 170 58 398 0.2 1 41 357 59 252 0.2 1 54 198 60 387 0.2 1 94 293 61 671 0.2 1 265 406 62 1050 0.2 1 470 580 63 741 0.2 1 256 485 64 269 0.2 1 71 198 65 164 0.2 1 23 141 66 306 0.2 1 33 273 67 246 0.2 1 29 217 68 221 0.2 1 28 193 69 216 0.2 1 29 187 70 222 0.2 1 24 198 71 242 0.2 1 27 215 72 207 0.2 1 24 183 73 222 0.2 1 19 203 74 202 0.2 1 22 180 75 330 0.2 1 32 298 76 261 0.2 1 22 239 77 247 0.2 1 29 218 78 193 0.2 1 25 168 79 191 0.2 1 13 178 80 181 0.2 1 19 162 81 163 0.2 1 15 148 82 163 0.2 1 11 152 83 225 0.2 1 26 199 84 222 0.2 1 27 195 85 199 0.2 1 19 180 86 132 0.2 1 22 110 87 112 0.2 1 15 97 88 131 0.2 1 12 119 89 152 0.2 1 23 129 90 124 0.2 1 9 115 91 100 0.2 1 9 91 92 129 0.2 1 13 116 93 116 0.2 1 14 102 94 134 0.2 1 10 124 95 70 0.2 1 7 63 96 82 0.2 1 5 77 97 76 0.2 1 9 67 98 70 0.2 1 7 63 99 71 0.2 1 8 63 100 77 0.2 1 9 68 101 57 0.2 1 6 51 102 89 0.2 1 11 78 103 45 0.2 1 11 34 104 38 0.2 1 8 30 105 34 0.2 1 5 29 106 31 0.2 1 5 26 107 22 0.2 1 4 18 108 26 0.2 1 7 19 109 30 0.2 1 8 22 110 56 0.2 1 15 41 111 12 0.2 1 7 5 112 5 0.2 1 1 4 113 4 0.2 1 4 114 15 0.2 1 4 11 115 11 0.2 1 9 2 116 21 0.2 1 9 12 117 5 0.2 1 5 118 9 0.2 1 8 1 119 10 0.2 1 10 120 3 0.2 1 3 121 12 0.2 1 9 3 122 7 0.2 1 7 123 16 0.2 1 12 4 124 13 0.2 1 9 4 125 26 0.2 1 23 3 126 54 0.2 1 41 13 127 66 0.2 1 56 10 128 95 0.2 1 84 11 129 87 0.2 1 75 12 130 90 0.2 1 72 18 131 106 0.2 1 92 14 132 110 0.2 1 97 13 133 191 0.2 1 169 22 134 293 0.2 1 264 29 135 811 0.2 1 741 70 136 2507 0.2 1 2175 332 137 97674 0.2 1 95135 2539 138 1972840 0.2 1 1940630 32210 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041601_val_2.fq.gz ============================================= 13633322 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 625476 (4.6%) 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: 13633322 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2144954 (15.73%)