SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041599_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/cd5bec26-5581-11eb-aec1-6c92bfc12bba/trimmed/RRBS20A041599_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 671.44 s (25 us/read; 2.41 M reads/minute). === Summary === Total reads processed: 26,999,619 Reads with adapters: 10,881,431 (40.3%) Reads written (passing filters): 26,999,619 (100.0%) Total basepairs processed: 2,668,431,962 bp Total written (filtered): 2,634,791,745 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10881431 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.7% C: 0.7% G: 20.2% T: 49.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7832513 6749904.8 0 7832513 2 2201234 1687476.2 0 2201234 3 510089 421869.0 0 510089 4 115053 105467.3 0 115053 5 8105 26366.8 0 8105 6 4507 6591.7 0 4507 7 3306 1647.9 0 3306 8 2905 412.0 0 2905 9 3931 103.0 0 3612 319 10 4092 25.7 1 2086 2006 11 1950 6.4 1 179 1771 12 793 1.6 1 96 697 13 790 0.4 1 103 687 14 1708 0.4 1 166 1542 15 1290 0.4 1 147 1143 16 3517 0.4 1 336 3181 17 3963 0.4 1 388 3575 18 1448 0.4 1 335 1113 19 89 0.4 1 4 85 20 700 0.4 1 85 615 21 85 0.4 1 5 80 22 113 0.4 1 15 98 23 890 0.4 1 98 792 24 2589 0.4 1 246 2343 25 1010 0.4 1 97 913 26 296 0.4 1 27 269 27 1071 0.4 1 127 944 28 2130 0.4 1 208 1922 29 2307 0.4 1 236 2071 30 343 0.4 1 54 289 31 100 0.4 1 5 95 32 714 0.4 1 74 640 33 1381 0.4 1 125 1256 34 1302 0.4 1 129 1173 35 2794 0.4 1 309 2485 36 1259 0.4 1 137 1122 37 373 0.4 1 36 337 38 1964 0.4 1 183 1781 39 561 0.4 1 52 509 40 2621 0.4 1 246 2375 41 1488 0.4 1 145 1343 42 1561 0.4 1 164 1397 43 2206 0.4 1 239 1967 44 582 0.4 1 65 517 45 1369 0.4 1 138 1231 46 504 0.4 1 45 459 47 861 0.4 1 83 778 48 2332 0.4 1 252 2080 49 464 0.4 1 49 415 50 927 0.4 1 123 804 51 377 0.4 1 36 341 52 361 0.4 1 32 329 53 696 0.4 1 86 610 54 2178 0.4 1 166 2012 55 1209 0.4 1 148 1061 56 758 0.4 1 72 686 57 886 0.4 1 90 796 58 606 0.4 1 73 533 59 414 0.4 1 47 367 60 601 0.4 1 51 550 61 863 0.4 1 75 788 62 1869 0.4 1 224 1645 63 573 0.4 1 63 510 64 89 0.4 1 9 80 65 54 0.4 1 8 46 66 290 0.4 1 23 267 67 287 0.4 1 26 261 68 836 0.4 1 59 777 69 1007 0.4 1 96 911 70 1624 0.4 1 185 1439 71 428 0.4 1 36 392 72 147 0.4 1 12 135 73 174 0.4 1 18 156 74 225 0.4 1 23 202 75 374 0.4 1 45 329 76 449 0.4 1 40 409 77 502 0.4 1 51 451 78 480 0.4 1 42 438 79 583 0.4 1 60 523 80 723 0.4 1 69 654 81 567 0.4 1 50 517 82 645 0.4 1 56 589 83 633 0.4 1 54 579 84 514 0.4 1 50 464 85 587 0.4 1 46 541 86 576 0.4 1 63 513 87 441 0.4 1 36 405 88 352 0.4 1 43 309 89 401 0.4 1 32 369 90 374 0.4 1 45 329 91 338 0.4 1 31 307 92 328 0.4 1 38 290 93 1276 0.4 1 109 1167 94 2193 0.4 1 161 2032 95 488 0.4 1 35 453 96 294 0.4 1 23 271 97 1944 0.4 1 133 1811 98 342 0.4 1 37 305 99 214 0.4 1 24 190 100 190 0.4 1 19 171 101 218 0.4 1 36 182 102 439 0.4 1 53 386 103 156 0.4 1 13 143 104 87 0.4 1 6 81 105 94 0.4 1 13 81 106 105 0.4 1 17 88 107 50 0.4 1 2 48 108 24 0.4 1 5 19 109 34 0.4 1 2 32 110 79 0.4 1 8 71 111 14 0.4 1 4 10 112 7 0.4 1 0 7 113 1 0.4 1 0 1 114 1 0.4 1 0 1 118 1 0.4 1 1 119 1 0.4 1 0 1 120 1 0.4 1 0 1 121 1 0.4 1 0 1 122 2 0.4 1 1 1 126 2 0.4 1 2 127 2 0.4 1 2 128 1 0.4 1 1 129 5 0.4 1 4 1 130 6 0.4 1 3 3 131 10 0.4 1 8 2 132 18 0.4 1 10 8 133 39 0.4 1 15 24 134 54 0.4 1 40 14 135 31 0.4 1 26 5 136 63 0.4 1 48 15 137 2935 0.4 1 2807 128 138 106405 0.4 1 103716 2689 140 4 0.4 1 0 4 142 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041599_val_1.fq.gz ============================================= 26999619 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1073424 (4.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 10881430 (40.3%)