SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041605_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/5aae55dc-48bc-11eb-8640-6c92bfc12e8a/trimmed/RRBS20A041605_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 305.01 s (22 us/read; 2.73 M reads/minute). === Summary === Total reads processed: 13,870,585 Reads with adapters: 5,630,311 (40.6%) Reads written (passing filters): 13,870,585 (100.0%) Total basepairs processed: 1,393,704,319 bp Total written (filtered): 1,379,817,738 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5630311 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 0.8% G: 21.7% T: 48.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4068848 3467646.2 0 4068848 2 1137556 866911.6 0 1137556 3 265864 216727.9 0 265864 4 59964 54182.0 0 59964 5 2943 13545.5 0 2943 6 1443 3386.4 0 1443 7 883 846.6 0 883 8 920 211.6 0 920 9 1558 52.9 0 1410 148 10 1396 13.2 1 474 922 11 1273 3.3 1 222 1051 12 550 0.8 1 100 450 13 636 0.2 1 121 515 14 1065 0.2 1 229 836 15 970 0.2 1 183 787 16 1844 0.2 1 335 1509 17 3605 0.2 1 796 2809 18 1167 0.2 1 256 911 19 68 0.2 1 7 61 20 614 0.2 1 123 491 21 78 0.2 1 11 67 22 104 0.2 1 15 89 23 494 0.2 1 88 406 24 1462 0.2 1 334 1128 25 731 0.2 1 166 565 26 198 0.2 1 36 162 27 740 0.2 1 129 611 28 1457 0.2 1 295 1162 29 1379 0.2 1 287 1092 30 361 0.2 1 82 279 31 51 0.2 1 8 43 32 657 0.2 1 136 521 33 891 0.2 1 156 735 34 860 0.2 1 184 676 35 1346 0.2 1 305 1041 36 388 0.2 1 68 320 37 474 0.2 1 84 390 38 905 0.2 1 186 719 39 812 0.2 1 168 644 40 393 0.2 1 87 306 41 1179 0.2 1 235 944 42 918 0.2 1 197 721 43 4016 0.2 1 870 3146 44 716 0.2 1 139 577 45 1115 0.2 1 236 879 46 344 0.2 1 61 283 47 562 0.2 1 108 454 48 1484 0.2 1 274 1210 49 155 0.2 1 32 123 50 848 0.2 1 190 658 51 251 0.2 1 46 205 52 161 0.2 1 27 134 53 580 0.2 1 114 466 54 2208 0.2 1 525 1683 55 1011 0.2 1 211 800 56 474 0.2 1 86 388 57 994 0.2 1 226 768 58 483 0.2 1 75 408 59 209 0.2 1 43 166 60 445 0.2 1 93 352 61 614 0.2 1 108 506 62 1626 0.2 1 379 1247 63 410 0.2 1 82 328 64 42 0.2 1 6 36 65 46 0.2 1 5 41 66 230 0.2 1 42 188 67 197 0.2 1 32 165 68 785 0.2 1 145 640 69 851 0.2 1 160 691 70 1543 0.2 1 370 1173 71 632 0.2 1 140 492 72 218 0.2 1 44 174 73 277 0.2 1 74 203 74 308 0.2 1 63 245 75 431 0.2 1 109 322 76 407 0.2 1 101 306 77 444 0.2 1 106 338 78 421 0.2 1 96 325 79 373 0.2 1 99 274 80 639 0.2 1 139 500 81 478 0.2 1 105 373 82 532 0.2 1 115 417 83 459 0.2 1 115 344 84 416 0.2 1 103 313 85 447 0.2 1 102 345 86 520 0.2 1 134 386 87 315 0.2 1 77 238 88 268 0.2 1 53 215 89 298 0.2 1 64 234 90 279 0.2 1 81 198 91 260 0.2 1 61 199 92 256 0.2 1 54 202 93 1260 0.2 1 327 933 94 2156 0.2 1 565 1591 95 546 0.2 1 129 417 96 289 0.2 1 61 228 97 2509 0.2 1 674 1835 98 236 0.2 1 56 180 99 138 0.2 1 39 99 100 143 0.2 1 28 115 101 116 0.2 1 30 86 102 227 0.2 1 65 162 103 77 0.2 1 22 55 104 45 0.2 1 17 28 105 41 0.2 1 9 32 106 48 0.2 1 14 34 107 33 0.2 1 15 18 108 12 0.2 1 2 10 109 14 0.2 1 0 14 110 16 0.2 1 7 9 111 2 0.2 1 1 1 112 4 0.2 1 1 3 113 1 0.2 1 0 1 115 5 0.2 1 1 4 116 4 0.2 1 1 3 117 1 0.2 1 1 121 1 0.2 1 1 126 1 0.2 1 1 127 1 0.2 1 1 128 1 0.2 1 1 130 2 0.2 1 1 1 131 1 0.2 1 1 132 3 0.2 1 1 2 133 6 0.2 1 3 3 134 5 0.2 1 5 135 8 0.2 1 7 1 136 32 0.2 1 29 3 137 6019 0.2 1 5886 133 138 16183 0.2 1 15739 444 140 2 0.2 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041605_val_1.fq.gz ============================================= 13870585 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 490301 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 5630310 (40.6%)