SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041612_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/20201118/tmp/691b5038-5592-11eb-9756-6c92bfc12ef6/trimmed/RRBS20A041612_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 680.16 s (29 us/read; 2.08 M reads/minute). === Summary === Total reads processed: 23,619,066 Reads with adapters: 8,443,796 (35.7%) Reads written (passing filters): 23,619,066 (100.0%) Total basepairs processed: 2,570,223,978 bp Total written (filtered): 2,555,258,744 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8443796 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 61.6% G: 0.8% T: 9.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8329660 5904766.5 0 8329660 2 29890 1476191.6 0 29890 3 4484 369047.9 0 4484 4 6400 92262.0 0 6400 5 1997 23065.5 0 1997 6 851 5766.4 0 851 7 1560 1441.6 0 1560 8 1772 360.4 0 1772 9 607 90.1 0 597 10 10 2105 22.5 1 326 1779 11 158 5.6 1 18 140 12 448 1.4 1 68 380 13 497 0.4 1 31 466 14 695 0.4 1 52 643 15 347 0.4 1 11 336 16 365 0.4 1 26 339 17 607 0.4 1 36 571 18 272 0.4 1 14 258 19 808 0.4 1 55 753 20 719 0.4 1 31 688 21 32 0.4 1 2 30 22 147 0.4 1 7 140 23 654 0.4 1 35 619 24 1534 0.4 1 86 1448 25 559 0.4 1 31 528 26 1392 0.4 1 61 1331 27 310 0.4 1 12 298 28 231 0.4 1 18 213 29 56 0.4 1 5 51 30 152 0.4 1 4 148 31 536 0.4 1 27 509 32 732 0.4 1 49 683 33 1596 0.4 1 76 1520 34 109 0.4 1 2 107 35 110 0.4 1 5 105 36 68 0.4 1 3 65 37 514 0.4 1 31 483 38 154 0.4 1 11 143 39 229 0.4 1 17 212 40 204 0.4 1 8 196 41 286 0.4 1 22 264 42 399 0.4 1 17 382 43 230 0.4 1 11 219 44 300 0.4 1 8 292 45 735 0.4 1 34 701 46 357 0.4 1 17 340 47 111 0.4 1 8 103 48 425 0.4 1 27 398 49 216 0.4 1 13 203 50 430 0.4 1 9 421 51 406 0.4 1 21 385 52 450 0.4 1 27 423 53 42 0.4 1 1 41 54 205 0.4 1 10 195 55 188 0.4 1 13 175 56 47 0.4 1 3 44 57 122 0.4 1 11 111 58 330 0.4 1 7 323 59 171 0.4 1 10 161 60 238 0.4 1 10 228 61 284 0.4 1 15 269 62 316 0.4 1 16 300 63 365 0.4 1 23 342 64 151 0.4 1 3 148 65 87 0.4 1 5 82 66 224 0.4 1 17 207 67 145 0.4 1 3 142 68 156 0.4 1 8 148 69 141 0.4 1 6 135 70 113 0.4 1 8 105 71 130 0.4 1 2 128 72 134 0.4 1 5 129 73 128 0.4 1 8 120 74 123 0.4 1 9 114 75 207 0.4 1 13 194 76 244 0.4 1 14 230 77 115 0.4 1 4 111 78 107 0.4 1 5 102 79 121 0.4 1 5 116 80 97 0.4 1 5 92 81 96 0.4 1 6 90 82 100 0.4 1 6 94 83 131 0.4 1 5 126 84 131 0.4 1 5 126 85 161 0.4 1 8 153 86 57 0.4 1 5 52 87 81 0.4 1 2 79 88 69 0.4 1 2 67 89 68 0.4 1 6 62 90 52 0.4 1 0 52 91 40 0.4 1 4 36 92 42 0.4 1 3 39 93 65 0.4 1 4 61 94 59 0.4 1 3 56 95 35 0.4 1 2 33 96 47 0.4 1 3 44 97 32 0.4 1 1 31 98 34 0.4 1 4 30 99 46 0.4 1 4 42 100 26 0.4 1 1 25 101 22 0.4 1 2 20 102 22 0.4 1 1 21 103 20 0.4 1 2 18 104 14 0.4 1 2 12 105 13 0.4 1 1 12 106 11 0.4 1 2 9 107 3 0.4 1 0 3 108 9 0.4 1 3 6 109 14 0.4 1 0 14 110 7 0.4 1 0 7 111 5 0.4 1 0 5 112 3 0.4 1 1 2 114 5 0.4 1 1 4 115 4 0.4 1 1 3 116 3 0.4 1 0 3 117 3 0.4 1 0 3 118 3 0.4 1 0 3 119 2 0.4 1 0 2 121 5 0.4 1 0 5 122 1 0.4 1 1 123 2 0.4 1 1 1 124 1 0.4 1 0 1 127 2 0.4 1 0 2 128 2 0.4 1 0 2 130 2 0.4 1 1 1 131 3 0.4 1 2 1 132 4 0.4 1 3 1 133 4 0.4 1 2 2 134 3 0.4 1 3 135 8 0.4 1 7 1 136 19 0.4 1 15 4 137 276 0.4 1 249 27 138 39292 0.4 1 38648 644 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041612_val_2.fq.gz ============================================= 23619066 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1117338 (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: 23619066 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 64186 (0.27%)