SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041583_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/20201104_20201106/tmp/6028bc46-48bc-11eb-95f7-6c92bfc12bd2/trimmed/RRBS20A041583_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 278.43 s (22 us/read; 2.75 M reads/minute). === Summary === Total reads processed: 12,744,424 Reads with adapters: 5,194,063 (40.8%) Reads written (passing filters): 12,744,424 (100.0%) Total basepairs processed: 1,260,220,182 bp Total written (filtered): 1,248,255,271 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5194063 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 0.5% G: 21.7% T: 47.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3760970 3186106.0 0 3760970 2 1054641 796526.5 0 1054641 3 242704 199131.6 0 242704 4 57425 49782.9 0 57425 5 4873 12445.7 0 4873 6 2100 3111.4 0 2100 7 1579 777.9 0 1579 8 1406 194.5 0 1406 9 1804 48.6 0 1610 194 10 1962 12.2 1 967 995 11 1095 3.0 1 122 973 12 454 0.8 1 60 394 13 438 0.2 1 57 381 14 662 0.2 1 69 593 15 710 0.2 1 85 625 16 1479 0.2 1 211 1268 17 2044 0.2 1 295 1749 18 1343 0.2 1 484 859 19 50 0.2 1 1 49 20 501 0.2 1 87 414 21 42 0.2 1 6 36 22 80 0.2 1 13 67 23 473 0.2 1 60 413 24 1125 0.2 1 117 1008 25 556 0.2 1 65 491 26 137 0.2 1 10 127 27 624 0.2 1 70 554 28 1142 0.2 1 161 981 29 1069 0.2 1 153 916 30 335 0.2 1 51 284 31 43 0.2 1 6 37 32 513 0.2 1 64 449 33 707 0.2 1 102 605 34 678 0.2 1 102 576 35 1092 0.2 1 130 962 36 291 0.2 1 35 256 37 362 0.2 1 39 323 38 701 0.2 1 65 636 39 624 0.2 1 78 546 40 299 0.2 1 40 259 41 826 0.2 1 96 730 42 602 0.2 1 67 535 43 2401 0.2 1 212 2189 44 485 0.2 1 43 442 45 680 0.2 1 63 617 46 229 0.2 1 23 206 47 419 0.2 1 51 368 48 928 0.2 1 106 822 49 105 0.2 1 7 98 50 562 0.2 1 60 502 51 156 0.2 1 16 140 52 118 0.2 1 18 100 53 313 0.2 1 39 274 54 918 0.2 1 97 821 55 417 0.2 1 50 367 56 321 0.2 1 33 288 57 436 0.2 1 50 386 58 318 0.2 1 34 284 59 149 0.2 1 14 135 60 306 0.2 1 47 259 61 389 0.2 1 44 345 62 849 0.2 1 109 740 63 270 0.2 1 25 245 64 44 0.2 1 9 35 65 41 0.2 1 7 34 66 134 0.2 1 13 121 67 156 0.2 1 21 135 68 539 0.2 1 53 486 69 575 0.2 1 73 502 70 1100 0.2 1 106 994 71 557 0.2 1 53 504 72 229 0.2 1 40 189 73 231 0.2 1 24 207 74 212 0.2 1 35 177 75 206 0.2 1 20 186 76 236 0.2 1 29 207 77 268 0.2 1 28 240 78 245 0.2 1 26 219 79 245 0.2 1 23 222 80 276 0.2 1 31 245 81 217 0.2 1 19 198 82 257 0.2 1 21 236 83 255 0.2 1 29 226 84 219 0.2 1 21 198 85 262 0.2 1 28 234 86 241 0.2 1 18 223 87 176 0.2 1 9 167 88 152 0.2 1 11 141 89 177 0.2 1 11 166 90 155 0.2 1 16 139 91 137 0.2 1 12 125 92 150 0.2 1 10 140 93 415 0.2 1 26 389 94 460 0.2 1 22 438 95 169 0.2 1 14 155 96 108 0.2 1 5 103 97 375 0.2 1 27 348 98 82 0.2 1 6 76 99 57 0.2 1 4 53 100 59 0.2 1 4 55 101 62 0.2 1 4 58 102 89 0.2 1 5 84 103 44 0.2 1 4 40 104 31 0.2 1 1 30 105 23 0.2 1 2 21 106 22 0.2 1 3 19 107 17 0.2 1 0 17 108 4 0.2 1 0 4 109 12 0.2 1 0 12 110 13 0.2 1 1 12 111 6 0.2 1 2 4 112 2 0.2 1 0 2 113 2 0.2 1 0 2 114 1 0.2 1 0 1 115 2 0.2 1 1 1 116 4 0.2 1 0 4 120 1 0.2 1 0 1 122 2 0.2 1 1 1 125 1 0.2 1 1 126 1 0.2 1 0 1 127 1 0.2 1 0 1 132 1 0.2 1 1 133 12 0.2 1 0 12 134 2 0.2 1 2 135 7 0.2 1 6 1 136 16 0.2 1 15 1 137 2709 0.2 1 2644 65 138 17210 0.2 1 16848 362 139 10 0.2 1 9 1 140 3009 0.2 1 2959 50 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041583_val_1.fq.gz ============================================= 12744424 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 436456 (3.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 5194062 (40.8%)