SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041601_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/c2f0e4d0-3f65-11eb-a7de-6c92bfc12c92/trimmed/RRBS20A041601_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 258.52 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 13,633,322 Reads with adapters: 6,730,765 (49.4%) Reads written (passing filters): 13,633,322 (100.0%) Total basepairs processed: 1,426,938,873 bp Total written (filtered): 1,130,518,465 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6730765 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.9% C: 0.6% G: 45.7% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3337820 3408330.5 0 3337820 2 962562 852082.6 0 962562 3 217883 213020.7 0 217883 4 52491 53255.2 0 52491 5 2928 13313.8 0 2928 6 1378 3328.4 0 1378 7 856 832.1 0 856 8 1091 208.0 0 1091 9 1449 52.0 0 1315 134 10 1401 13.0 1 554 847 11 1105 3.3 1 180 925 12 468 0.8 1 74 394 13 526 0.2 1 82 444 14 903 0.2 1 163 740 15 988 0.2 1 175 813 16 1952 0.2 1 372 1580 17 4620 0.2 1 1932 2688 18 7378 0.2 1 5836 1542 19 98 0.2 1 32 66 20 609 0.2 1 182 427 21 64 0.2 1 13 51 22 101 0.2 1 37 64 23 489 0.2 1 71 418 24 1450 0.2 1 309 1141 25 765 0.2 1 201 564 26 230 0.2 1 43 187 27 702 0.2 1 150 552 28 1461 0.2 1 412 1049 29 1358 0.2 1 281 1077 30 331 0.2 1 66 265 31 67 0.2 1 7 60 32 642 0.2 1 133 509 33 1020 0.2 1 171 849 34 982 0.2 1 184 798 35 1560 0.2 1 350 1210 36 388 0.2 1 72 316 37 1483 0.2 1 450 1033 38 369 0.2 1 176 193 39 660 0.2 1 129 531 40 182 0.2 1 54 128 41 1368 0.2 1 247 1121 42 668 0.2 1 123 545 43 1918 0.2 1 392 1526 44 470 0.2 1 91 379 45 945 0.2 1 176 769 46 236 0.2 1 42 194 47 593 0.2 1 99 494 48 1329 0.2 1 279 1050 49 89 0.2 1 10 79 50 827 0.2 1 142 685 51 219 0.2 1 55 164 52 166 0.2 1 26 140 53 682 0.2 1 145 537 54 2045 0.2 1 452 1593 55 1124 0.2 1 254 870 56 457 0.2 1 92 365 57 1102 0.2 1 241 861 58 541 0.2 1 96 445 59 176 0.2 1 33 143 60 505 0.2 1 92 413 61 643 0.2 1 121 522 62 1680 0.2 1 378 1302 63 500 0.2 1 115 385 64 29 0.2 1 8 21 65 41 0.2 1 8 33 66 196 0.2 1 37 159 67 217 0.2 1 37 180 68 875 0.2 1 168 707 69 899 0.2 1 178 721 70 1586 0.2 1 343 1243 71 468 0.2 1 88 380 72 232 0.2 1 43 189 73 262 0.2 1 57 205 74 316 0.2 1 69 247 75 491 0.2 1 122 369 76 413 0.2 1 118 295 77 456 0.2 1 78 378 78 516 0.2 1 126 390 79 435 0.2 1 111 324 80 551 0.2 1 117 434 81 488 0.2 1 113 375 82 523 0.2 1 131 392 83 501 0.2 1 87 414 84 464 0.2 1 120 344 85 507 0.2 1 111 396 86 558 0.2 1 170 388 87 296 0.2 1 55 241 88 314 0.2 1 55 259 89 347 0.2 1 71 276 90 313 0.2 1 91 222 91 288 0.2 1 82 206 92 321 0.2 1 79 242 93 1316 0.2 1 314 1002 94 1914 0.2 1 408 1506 95 500 0.2 1 117 383 96 380 0.2 1 123 257 97 2144 0.2 1 463 1681 98 242 0.2 1 52 190 99 158 0.2 1 34 124 100 174 0.2 1 45 129 101 196 0.2 1 52 144 102 323 0.2 1 77 246 103 144 0.2 1 36 108 104 78 0.2 1 20 58 105 90 0.2 1 18 72 106 96 0.2 1 28 68 107 54 0.2 1 14 40 108 19 0.2 1 5 14 109 25 0.2 1 12 13 110 62 0.2 1 13 49 111 10 0.2 1 3 7 112 12 0.2 1 7 5 113 4 0.2 1 1 3 114 22 0.2 1 4 18 115 19 0.2 1 10 9 116 48 0.2 1 12 36 117 9 0.2 1 6 3 118 8 0.2 1 7 1 119 4 0.2 1 4 120 5 0.2 1 3 2 121 12 0.2 1 8 4 122 12 0.2 1 9 3 123 11 0.2 1 9 2 124 20 0.2 1 17 3 125 19 0.2 1 19 126 31 0.2 1 21 10 127 26 0.2 1 21 5 128 51 0.2 1 42 9 129 68 0.2 1 52 16 130 78 0.2 1 62 16 131 72 0.2 1 59 13 132 158 0.2 1 129 29 133 352 0.2 1 287 65 134 596 0.2 1 486 110 135 764 0.2 1 636 128 136 1701 0.2 1 1309 392 137 93969 0.2 1 90966 3003 138 1980760 0.2 1 1909145 71615 139 9 0.2 1 4 5 140 3 0.2 1 0 3 143 1 0.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041601_val_1.fq.gz ============================================= 13633322 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 438221 (3.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6730753 (49.4%)