SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041607_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/20201120/tmp/a700d9c4-5572-11eb-ad2c-6c92bfc3978c/trimmed/RRBS20A041607_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 457.67 s (22 us/read; 2.75 M reads/minute). === Summary === Total reads processed: 21,011,298 Reads with adapters: 8,777,889 (41.8%) Reads written (passing filters): 21,011,298 (100.0%) Total basepairs processed: 2,135,648,748 bp Total written (filtered): 2,047,659,936 bp (95.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8777889 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.7% C: 7.3% G: 18.3% T: 45.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5989648 5252824.5 0 5989648 2 1712011 1313206.1 0 1712011 3 368975 328301.5 0 368975 4 87210 82075.4 0 87210 5 4933 20518.8 0 4933 6 2566 5129.7 0 2566 7 1859 1282.4 0 1859 8 1691 320.6 0 1691 9 2209 80.2 0 1941 268 10 2717 20.0 1 1073 1644 11 1517 5.0 1 191 1326 12 752 1.3 1 113 639 13 612 0.3 1 75 537 14 1416 0.3 1 187 1229 15 1055 0.3 1 154 901 16 3215 0.3 1 847 2368 17 2762 0.3 1 377 2385 18 1489 0.3 1 198 1291 19 86 0.3 1 11 75 20 576 0.3 1 91 485 21 118 0.3 1 8 110 22 181 0.3 1 29 152 23 607 0.3 1 82 525 24 2045 0.3 1 334 1711 25 948 0.3 1 164 784 26 389 0.3 1 56 333 27 915 0.3 1 114 801 28 1941 0.3 1 281 1660 29 1858 0.3 1 269 1589 30 543 0.3 1 76 467 31 183 0.3 1 17 166 32 938 0.3 1 144 794 33 1659 0.3 1 261 1398 34 1678 0.3 1 252 1426 35 1228 0.3 1 151 1077 36 800 0.3 1 116 684 37 1224 0.3 1 204 1020 38 310 0.3 1 40 270 39 194 0.3 1 35 159 40 876 0.3 1 103 773 41 581 0.3 1 87 494 42 1127 0.3 1 150 977 43 1757 0.3 1 226 1531 44 381 0.3 1 59 322 45 819 0.3 1 110 709 46 314 0.3 1 43 271 47 552 0.3 1 58 494 48 1677 0.3 1 207 1470 49 165 0.3 1 17 148 50 799 0.3 1 99 700 51 301 0.3 1 38 263 52 234 0.3 1 36 198 53 622 0.3 1 83 539 54 2382 0.3 1 280 2102 55 1254 0.3 1 168 1086 56 687 0.3 1 94 593 57 941 0.3 1 132 809 58 632 0.3 1 71 561 59 282 0.3 1 23 259 60 481 0.3 1 46 435 61 764 0.3 1 99 665 62 1869 0.3 1 258 1611 63 502 0.3 1 67 435 64 74 0.3 1 5 69 65 44 0.3 1 7 37 66 216 0.3 1 23 193 67 196 0.3 1 19 177 68 811 0.3 1 104 707 69 897 0.3 1 117 780 70 1614 0.3 1 223 1391 71 676 0.3 1 83 593 72 264 0.3 1 28 236 73 410 0.3 1 47 363 74 331 0.3 1 41 290 75 468 0.3 1 74 394 76 399 0.3 1 45 354 77 494 0.3 1 54 440 78 379 0.3 1 48 331 79 447 0.3 1 60 387 80 550 0.3 1 65 485 81 406 0.3 1 51 355 82 451 0.3 1 55 396 83 503 0.3 1 81 422 84 345 0.3 1 47 298 85 373 0.3 1 44 329 86 564 0.3 1 81 483 87 284 0.3 1 37 247 88 263 0.3 1 33 230 89 295 0.3 1 38 257 90 275 0.3 1 27 248 91 234 0.3 1 31 203 92 258 0.3 1 39 219 93 1335 0.3 1 170 1165 94 1761 0.3 1 177 1584 95 438 0.3 1 52 386 96 270 0.3 1 37 233 97 1646 0.3 1 185 1461 98 211 0.3 1 31 180 99 117 0.3 1 18 99 100 117 0.3 1 10 107 101 169 0.3 1 25 144 102 312 0.3 1 62 250 103 86 0.3 1 7 79 104 48 0.3 1 7 41 105 49 0.3 1 8 41 106 74 0.3 1 13 61 107 32 0.3 1 4 28 108 10 0.3 1 2 8 109 26 0.3 1 5 21 110 35 0.3 1 5 30 111 13 0.3 1 4 9 112 4 0.3 1 1 3 113 2 0.3 1 1 1 114 6 0.3 1 3 3 116 1 0.3 1 0 1 117 2 0.3 1 2 118 1 0.3 1 1 119 3 0.3 1 0 3 121 3 0.3 1 1 2 122 3 0.3 1 2 1 123 5 0.3 1 4 1 124 2 0.3 1 2 125 3 0.3 1 3 126 3 0.3 1 3 127 3 0.3 1 2 1 128 8 0.3 1 6 2 129 9 0.3 1 7 2 130 20 0.3 1 15 5 131 18 0.3 1 14 4 132 28 0.3 1 25 3 133 77 0.3 1 58 19 134 124 0.3 1 98 26 135 178 0.3 1 138 40 136 294 0.3 1 253 41 137 9993 0.3 1 9597 396 138 522765 0.3 1 511399 11366 140 7 0.3 1 0 7 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041607_val_1.fq.gz ============================================= 21011298 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 853126 (4.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 8777884 (41.8%)