SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041520_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/20201115/tmp/44eb47b0-3e8e-11eb-b3f9-b4055d0383c6/trimmed/RRBS20A041520_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 2952.51 s (64 us/read; 0.94 M reads/minute). === Summary === Total reads processed: 46,233,883 Reads with adapters: 15,354,367 (33.2%) Reads written (passing filters): 46,233,883 (100.0%) Total basepairs processed: 4,682,187,564 bp Total written (filtered): 4,643,761,811 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15354367 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.3% C: 71.9% G: 0.9% T: 7.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15011369 11558470.8 0 15011369 2 79198 2889617.7 0 79198 3 20064 722404.4 0 20064 4 19207 180601.1 0 19207 5 3525 45150.3 0 3525 6 1778 11287.6 0 1778 7 2509 2821.9 0 2509 8 1878 705.5 0 1878 9 1243 176.4 0 1198 45 10 5177 44.1 1 1027 4150 11 488 11.0 1 89 399 12 1091 2.8 1 142 949 13 1037 0.7 1 104 933 14 1631 0.7 1 199 1432 15 615 0.7 1 52 563 16 807 0.7 1 95 712 17 1194 0.7 1 128 1066 18 504 0.7 1 42 462 19 1697 0.7 1 183 1514 20 1320 0.7 1 129 1191 21 63 0.7 1 3 60 22 249 0.7 1 26 223 23 1232 0.7 1 138 1094 24 2959 0.7 1 317 2642 25 1115 0.7 1 91 1024 26 2152 0.7 1 170 1982 27 1358 0.7 1 128 1230 28 989 0.7 1 103 886 29 131 0.7 1 16 115 30 224 0.7 1 19 205 31 241 0.7 1 24 217 32 1184 0.7 1 137 1047 33 2849 0.7 1 331 2518 34 615 0.7 1 53 562 35 535 0.7 1 58 477 36 144 0.7 1 16 128 37 1476 0.7 1 145 1331 38 367 0.7 1 36 331 39 520 0.7 1 46 474 40 435 0.7 1 51 384 41 483 0.7 1 35 448 42 822 0.7 1 80 742 43 498 0.7 1 41 457 44 685 0.7 1 75 610 45 1682 0.7 1 173 1509 46 852 0.7 1 77 775 47 267 0.7 1 27 240 48 905 0.7 1 74 831 49 611 0.7 1 71 540 50 770 0.7 1 89 681 51 1041 0.7 1 101 940 52 1197 0.7 1 138 1059 53 121 0.7 1 9 112 54 603 0.7 1 45 558 55 600 0.7 1 65 535 56 120 0.7 1 10 110 57 512 0.7 1 54 458 58 868 0.7 1 80 788 59 583 0.7 1 65 518 60 781 0.7 1 85 696 61 956 0.7 1 94 862 62 1270 0.7 1 126 1144 63 1209 0.7 1 135 1074 64 400 0.7 1 37 363 65 301 0.7 1 20 281 66 883 0.7 1 105 778 67 528 0.7 1 38 490 68 490 0.7 1 43 447 69 466 0.7 1 47 419 70 534 0.7 1 40 494 71 485 0.7 1 36 449 72 501 0.7 1 60 441 73 525 0.7 1 49 476 74 511 0.7 1 41 470 75 1264 0.7 1 151 1113 76 1062 0.7 1 105 957 77 706 0.7 1 72 634 78 391 0.7 1 31 360 79 454 0.7 1 41 413 80 451 0.7 1 39 412 81 435 0.7 1 39 396 82 474 0.7 1 37 437 83 462 0.7 1 34 428 84 491 0.7 1 51 440 85 467 0.7 1 40 427 86 353 0.7 1 34 319 87 260 0.7 1 22 238 88 263 0.7 1 23 240 89 277 0.7 1 31 246 90 216 0.7 1 17 199 91 183 0.7 1 12 171 92 196 0.7 1 18 178 93 261 0.7 1 18 243 94 270 0.7 1 27 243 95 159 0.7 1 19 140 96 195 0.7 1 15 180 97 202 0.7 1 20 182 98 143 0.7 1 13 130 99 173 0.7 1 15 158 100 187 0.7 1 15 172 101 151 0.7 1 13 138 102 197 0.7 1 19 178 103 105 0.7 1 8 97 104 44 0.7 1 5 39 105 48 0.7 1 5 43 106 34 0.7 1 5 29 107 26 0.7 1 3 23 108 23 0.7 1 2 21 109 84 0.7 1 8 76 110 18 0.7 1 2 16 111 4 0.7 1 0 4 112 1 0.7 1 0 1 114 4 0.7 1 2 2 115 3 0.7 1 0 3 118 4 0.7 1 3 1 122 2 0.7 1 2 123 1 0.7 1 1 125 1 0.7 1 1 126 2 0.7 1 2 127 1 0.7 1 1 128 4 0.7 1 4 129 4 0.7 1 4 130 2 0.7 1 2 131 4 0.7 1 4 132 3 0.7 1 1 2 133 7 0.7 1 5 2 134 6 0.7 1 5 1 135 22 0.7 1 21 1 136 69 0.7 1 58 11 137 1914 0.7 1 1833 81 138 143354 0.7 1 140792 2562 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041520_val_2.fq.gz ============================================= 46233883 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2190434 (4.7%) 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: 46233883 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 281068 (0.61%)