SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041629_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/a593f6f2-5572-11eb-abe2-6c92bfc1231a/trimmed/RRBS20A041629_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 825.31 s (23 us/read; 2.65 M reads/minute). === Summary === Total reads processed: 36,466,929 Reads with adapters: 13,409,243 (36.8%) Reads written (passing filters): 36,466,929 (100.0%) Total basepairs processed: 3,615,549,305 bp Total written (filtered): 3,418,309,236 bp (94.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13409243 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.6% C: 67.2% G: 0.8% T: 15.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11904366 9116732.2 0 11904366 2 75797 2279183.1 0 75797 3 16812 569795.8 0 16812 4 15921 142448.9 0 15921 5 3223 35612.2 0 3223 6 1551 8903.1 0 1551 7 2381 2225.8 0 2381 8 1587 556.4 0 1587 9 1056 139.1 0 1004 52 10 4653 34.8 1 901 3752 11 484 8.7 1 78 406 12 988 2.2 1 98 890 13 1180 0.5 1 127 1053 14 1355 0.5 1 147 1208 15 509 0.5 1 53 456 16 788 0.5 1 73 715 17 1074 0.5 1 114 960 18 417 0.5 1 38 379 19 1508 0.5 1 157 1351 20 1160 0.5 1 145 1015 21 90 0.5 1 33 57 22 239 0.5 1 17 222 23 1187 0.5 1 135 1052 24 2798 0.5 1 301 2497 25 1102 0.5 1 98 1004 26 1906 0.5 1 201 1705 27 1473 0.5 1 149 1324 28 1125 0.5 1 179 946 29 156 0.5 1 19 137 30 304 0.5 1 28 276 31 224 0.5 1 18 206 32 1253 0.5 1 146 1107 33 2397 0.5 1 255 2142 34 733 0.5 1 92 641 35 620 0.5 1 62 558 36 171 0.5 1 18 153 37 1175 0.5 1 118 1057 38 413 0.5 1 48 365 39 540 0.5 1 53 487 40 559 0.5 1 62 497 41 610 0.5 1 65 545 42 1028 0.5 1 120 908 43 543 0.5 1 60 483 44 812 0.5 1 80 732 45 1466 0.5 1 155 1311 46 662 0.5 1 71 591 47 353 0.5 1 34 319 48 855 0.5 1 96 759 49 689 0.5 1 77 612 50 1147 0.5 1 136 1011 51 1189 0.5 1 124 1065 52 1224 0.5 1 134 1090 53 142 0.5 1 16 126 54 557 0.5 1 53 504 55 696 0.5 1 92 604 56 144 0.5 1 17 127 57 458 0.5 1 36 422 58 886 0.5 1 78 808 59 562 0.5 1 68 494 60 832 0.5 1 105 727 61 1086 0.5 1 173 913 62 1458 0.5 1 283 1175 63 1383 0.5 1 273 1110 64 476 0.5 1 67 409 65 376 0.5 1 62 314 66 1328 0.5 1 137 1191 67 633 0.5 1 75 558 68 553 0.5 1 69 484 69 463 0.5 1 53 410 70 519 0.5 1 53 466 71 562 0.5 1 54 508 72 479 0.5 1 54 425 73 486 0.5 1 47 439 74 518 0.5 1 67 451 75 780 0.5 1 92 688 76 871 0.5 1 101 770 77 559 0.5 1 68 491 78 379 0.5 1 42 337 79 434 0.5 1 53 381 80 456 0.5 1 48 408 81 413 0.5 1 37 376 82 481 0.5 1 45 436 83 535 0.5 1 60 475 84 482 0.5 1 54 428 85 554 0.5 1 49 505 86 361 0.5 1 40 321 87 290 0.5 1 36 254 88 256 0.5 1 37 219 89 252 0.5 1 31 221 90 252 0.5 1 36 216 91 242 0.5 1 27 215 92 217 0.5 1 20 197 93 262 0.5 1 28 234 94 240 0.5 1 28 212 95 135 0.5 1 25 110 96 167 0.5 1 27 140 97 148 0.5 1 20 128 98 124 0.5 1 11 113 99 133 0.5 1 18 115 100 120 0.5 1 18 102 101 121 0.5 1 19 102 102 120 0.5 1 12 108 103 84 0.5 1 14 70 104 57 0.5 1 11 46 105 53 0.5 1 8 45 106 50 0.5 1 6 44 107 23 0.5 1 3 20 108 35 0.5 1 9 26 109 46 0.5 1 12 34 110 31 0.5 1 5 26 111 16 0.5 1 5 11 112 13 0.5 1 8 5 113 13 0.5 1 5 8 114 23 0.5 1 10 13 115 7 0.5 1 7 116 9 0.5 1 5 4 117 11 0.5 1 8 3 118 11 0.5 1 8 3 119 8 0.5 1 6 2 120 14 0.5 1 12 2 121 14 0.5 1 8 6 122 7 0.5 1 6 1 123 10 0.5 1 4 6 124 8 0.5 1 8 125 16 0.5 1 12 4 126 27 0.5 1 21 6 127 25 0.5 1 17 8 128 45 0.5 1 37 8 129 35 0.5 1 26 9 130 39 0.5 1 29 10 131 53 0.5 1 44 9 132 51 0.5 1 40 11 133 102 0.5 1 79 23 134 116 0.5 1 90 26 135 305 0.5 1 241 64 136 721 0.5 1 615 106 137 7010 0.5 1 6465 545 138 1310315 0.5 1 1284210 26105 139 6 0.5 1 2 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041629_val_2.fq.gz ============================================= 36466929 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1791694 (4.9%) 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: 36466929 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1432124 (3.93%)