SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041606_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/20201118/tmp/68a4493e-5592-11eb-92b6-6c92bfc12f0e/trimmed/RRBS20A041606_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 165.20 s (23 us/read; 2.61 M reads/minute). === Summary === Total reads processed: 7,181,082 Reads with adapters: 3,076,912 (42.8%) Reads written (passing filters): 7,181,082 (100.0%) Total basepairs processed: 793,225,383 bp Total written (filtered): 776,840,855 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3076912 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 0.8% G: 22.4% T: 49.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2200320 1795270.5 0 2200320 2 584832 448817.6 0 584832 3 142882 112204.4 0 142882 4 31214 28051.1 0 31214 5 1885 7012.8 0 1885 6 796 1753.2 0 796 7 691 438.3 0 691 8 525 109.6 0 525 9 997 27.4 0 888 109 10 982 6.8 1 289 693 11 967 1.7 1 99 868 12 339 0.4 1 33 306 13 331 0.1 1 47 284 14 655 0.1 1 80 575 15 479 0.1 1 62 417 16 1586 0.1 1 205 1381 17 2249 0.1 1 751 1498 18 2227 0.1 1 1635 592 19 27 0.1 1 8 19 20 398 0.1 1 67 331 21 27 0.1 1 1 26 22 47 0.1 1 7 40 23 308 0.1 1 33 275 24 1159 0.1 1 159 1000 25 460 0.1 1 51 409 26 166 0.1 1 16 150 27 432 0.1 1 63 369 28 924 0.1 1 113 811 29 1030 0.1 1 167 863 30 197 0.1 1 23 174 31 38 0.1 1 3 35 32 413 0.1 1 48 365 33 709 0.1 1 89 620 34 819 0.1 1 115 704 35 389 0.1 1 52 337 36 411 0.1 1 44 367 37 671 0.1 1 93 578 38 224 0.1 1 24 200 39 90 0.1 1 17 73 40 566 0.1 1 73 493 41 363 0.1 1 41 322 42 571 0.1 1 80 491 43 988 0.1 1 162 826 44 144 0.1 1 14 130 45 409 0.1 1 49 360 46 92 0.1 1 16 76 47 263 0.1 1 35 228 48 677 0.1 1 93 584 49 48 0.1 1 3 45 50 407 0.1 1 59 348 51 111 0.1 1 19 92 52 63 0.1 1 6 57 53 214 0.1 1 22 192 54 640 0.1 1 96 544 55 360 0.1 1 51 309 56 195 0.1 1 20 175 57 327 0.1 1 44 283 58 166 0.1 1 22 144 59 94 0.1 1 12 82 60 161 0.1 1 17 144 61 178 0.1 1 19 159 62 601 0.1 1 88 513 63 151 0.1 1 21 130 64 16 0.1 1 1 15 65 5 0.1 1 1 4 66 64 0.1 1 11 53 67 60 0.1 1 7 53 68 245 0.1 1 30 215 69 244 0.1 1 38 206 70 554 0.1 1 65 489 71 186 0.1 1 24 162 72 40 0.1 1 5 35 73 95 0.1 1 10 85 74 99 0.1 1 17 82 75 98 0.1 1 17 81 76 140 0.1 1 24 116 77 159 0.1 1 28 131 78 112 0.1 1 11 101 79 93 0.1 1 16 77 80 162 0.1 1 24 138 81 108 0.1 1 18 90 82 153 0.1 1 27 126 83 154 0.1 1 28 126 84 127 0.1 1 11 116 85 190 0.1 1 36 154 86 92 0.1 1 8 84 87 88 0.1 1 4 84 88 60 0.1 1 5 55 89 95 0.1 1 20 75 90 76 0.1 1 12 64 91 62 0.1 1 11 51 92 73 0.1 1 12 61 93 163 0.1 1 12 151 94 329 0.1 1 28 301 95 117 0.1 1 14 103 96 49 0.1 1 7 42 97 183 0.1 1 11 172 98 48 0.1 1 6 42 99 49 0.1 1 8 41 100 33 0.1 1 2 31 101 33 0.1 1 5 28 102 65 0.1 1 8 57 103 25 0.1 1 7 18 104 12 0.1 1 1 11 105 15 0.1 1 1 14 106 9 0.1 1 1 8 107 5 0.1 1 0 5 108 6 0.1 1 1 5 109 3 0.1 1 0 3 110 3 0.1 1 0 3 111 1 0.1 1 0 1 112 2 0.1 1 1 1 116 2 0.1 1 0 2 117 1 0.1 1 1 120 1 0.1 1 0 1 122 1 0.1 1 0 1 124 1 0.1 1 1 125 1 0.1 1 0 1 126 1 0.1 1 0 1 127 2 0.1 1 2 130 1 0.1 1 1 131 2 0.1 1 2 132 6 0.1 1 3 3 133 16 0.1 1 6 10 134 26 0.1 1 23 3 135 17 0.1 1 14 3 136 24 0.1 1 20 4 137 548 0.1 1 518 30 138 80777 0.1 1 79207 1570 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/182021/20201118/RRBS20A041606_val_1.fq.gz ============================================= 7181082 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 245718 (3.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 3076912 (42.8%)