SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041610_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/20201110/tmp/c90756ec-5581-11eb-8caf-6c92bfc39744/trimmed/RRBS20A041610_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 217.97 s (23 us/read; 2.66 M reads/minute). === Summary === Total reads processed: 9,676,956 Reads with adapters: 4,073,472 (42.1%) Reads written (passing filters): 9,676,956 (100.0%) Total basepairs processed: 988,222,338 bp Total written (filtered): 956,572,474 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4073472 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.0% C: 0.8% G: 24.9% T: 46.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2810838 2419239.0 0 2810838 2 787511 604809.8 0 787511 3 190885 151202.4 0 190885 4 43986 37800.6 0 43986 5 3416 9450.2 0 3416 6 2268 2362.5 0 2268 7 1623 590.6 0 1623 8 1628 147.7 0 1628 9 2370 36.9 0 2210 160 10 1883 9.2 1 1106 777 11 1154 2.3 1 168 986 12 405 0.6 1 66 339 13 523 0.1 1 99 424 14 971 0.1 1 160 811 15 697 0.1 1 128 569 16 2303 0.1 1 407 1896 17 2516 0.1 1 557 1959 18 1483 0.1 1 807 676 19 60 0.1 1 6 54 20 493 0.1 1 110 383 21 45 0.1 1 6 39 22 70 0.1 1 5 65 23 646 0.1 1 120 526 24 1677 0.1 1 328 1349 25 648 0.1 1 117 531 26 181 0.1 1 29 152 27 626 0.1 1 115 511 28 1433 0.1 1 287 1146 29 1555 0.1 1 266 1289 30 221 0.1 1 38 183 31 52 0.1 1 12 40 32 460 0.1 1 86 374 33 925 0.1 1 176 749 34 874 0.1 1 162 712 35 1804 0.1 1 406 1398 36 760 0.1 1 144 616 37 243 0.1 1 53 190 38 1240 0.1 1 263 977 39 395 0.1 1 69 326 40 1668 0.1 1 316 1352 41 921 0.1 1 168 753 42 996 0.1 1 212 784 43 1388 0.1 1 264 1124 44 360 0.1 1 63 297 45 874 0.1 1 166 708 46 340 0.1 1 51 289 47 567 0.1 1 103 464 48 1495 0.1 1 323 1172 49 259 0.1 1 44 215 50 621 0.1 1 117 504 51 250 0.1 1 43 207 52 192 0.1 1 30 162 53 445 0.1 1 83 362 54 1288 0.1 1 270 1018 55 669 0.1 1 154 515 56 497 0.1 1 88 409 57 516 0.1 1 90 426 58 349 0.1 1 73 276 59 266 0.1 1 56 210 60 308 0.1 1 62 246 61 435 0.1 1 79 356 62 1023 0.1 1 262 761 63 285 0.1 1 62 223 64 39 0.1 1 7 32 65 35 0.1 1 2 33 66 135 0.1 1 21 114 67 139 0.1 1 23 116 68 548 0.1 1 110 438 69 668 0.1 1 125 543 70 1087 0.1 1 207 880 71 278 0.1 1 64 214 72 110 0.1 1 22 88 73 92 0.1 1 15 77 74 140 0.1 1 34 106 75 217 0.1 1 47 170 76 255 0.1 1 60 195 77 338 0.1 1 86 252 78 339 0.1 1 76 263 79 343 0.1 1 71 272 80 470 0.1 1 101 369 81 343 0.1 1 79 264 82 372 0.1 1 70 302 83 376 0.1 1 86 290 84 273 0.1 1 42 231 85 374 0.1 1 83 291 86 311 0.1 1 55 256 87 256 0.1 1 44 212 88 226 0.1 1 57 169 89 243 0.1 1 51 192 90 210 0.1 1 37 173 91 203 0.1 1 52 151 92 162 0.1 1 33 129 93 483 0.1 1 121 362 94 979 0.1 1 204 775 95 250 0.1 1 58 192 96 205 0.1 1 44 161 97 979 0.1 1 216 763 98 180 0.1 1 40 140 99 110 0.1 1 29 81 100 103 0.1 1 30 73 101 81 0.1 1 11 70 102 164 0.1 1 40 124 103 64 0.1 1 15 49 104 42 0.1 1 14 28 105 52 0.1 1 11 41 106 34 0.1 1 9 25 107 33 0.1 1 10 23 108 11 0.1 1 1 10 109 14 0.1 1 5 9 110 22 0.1 1 3 19 111 10 0.1 1 4 6 112 6 0.1 1 2 4 113 2 0.1 1 0 2 114 1 0.1 1 1 115 3 0.1 1 0 3 116 8 0.1 1 2 6 117 1 0.1 1 1 121 3 0.1 1 3 122 4 0.1 1 2 2 123 6 0.1 1 6 127 3 0.1 1 2 1 128 4 0.1 1 4 129 6 0.1 1 4 2 130 14 0.1 1 11 3 131 20 0.1 1 17 3 132 32 0.1 1 23 9 133 55 0.1 1 41 14 134 83 0.1 1 75 8 135 76 0.1 1 64 12 136 239 0.1 1 204 35 137 34677 0.1 1 33711 966 138 138943 0.1 1 134697 4246 139 3 0.1 1 2 1 140 5 0.1 1 0 5 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041610_val_1.fq.gz ============================================= 9676956 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 364829 (3.8%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 4073472 (42.1%)