SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041626_val_2.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/599d18b8-48bc-11eb-aad8-6c92bfbea1ec/trimmed/RRBS20A041626_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 926.09 s (23 us/read; 2.64 M reads/minute). === Summary === Total reads processed: 40,788,920 Reads with adapters: 13,840,476 (33.9%) Reads written (passing filters): 40,788,920 (100.0%) Total basepairs processed: 4,070,137,372 bp Total written (filtered): 4,049,917,808 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13840476 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.7% C: 74.7% G: 1.5% T: 6.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13616405 10197230.0 0 13616405 2 80196 2549307.5 0 80196 3 14889 637326.9 0 14889 4 11220 159331.7 0 11220 5 3867 39832.9 0 3867 6 2149 9958.2 0 2149 7 3197 2489.6 0 3197 8 2393 622.4 0 2393 9 1299 155.6 0 1256 43 10 5605 38.9 1 1368 4237 11 497 9.7 1 111 386 12 1126 2.4 1 189 937 13 1406 0.6 1 193 1213 14 2084 0.6 1 284 1800 15 786 0.6 1 98 688 16 1094 0.6 1 153 941 17 1619 0.6 1 192 1427 18 640 0.6 1 79 561 19 1833 0.6 1 263 1570 20 1580 0.6 1 207 1373 21 76 0.6 1 7 69 22 306 0.6 1 42 264 23 1513 0.6 1 181 1332 24 3998 0.6 1 537 3461 25 1536 0.6 1 182 1354 26 2783 0.6 1 356 2427 27 1821 0.6 1 250 1571 28 1526 0.6 1 235 1291 29 184 0.6 1 21 163 30 390 0.6 1 50 340 31 295 0.6 1 28 267 32 1437 0.6 1 204 1233 33 3358 0.6 1 424 2934 34 890 0.6 1 118 772 35 790 0.6 1 115 675 36 216 0.6 1 20 196 37 1816 0.6 1 237 1579 38 616 0.6 1 76 540 39 669 0.6 1 84 585 40 751 0.6 1 99 652 41 714 0.6 1 87 627 42 1175 0.6 1 154 1021 43 664 0.6 1 89 575 44 851 0.6 1 86 765 45 1954 0.6 1 227 1727 46 1019 0.6 1 112 907 47 407 0.6 1 41 366 48 1301 0.6 1 152 1149 49 870 0.6 1 136 734 50 1402 0.6 1 188 1214 51 1452 0.6 1 210 1242 52 1602 0.6 1 189 1413 53 181 0.6 1 27 154 54 835 0.6 1 90 745 55 996 0.6 1 136 860 56 146 0.6 1 18 128 57 651 0.6 1 74 577 58 1147 0.6 1 123 1024 59 683 0.6 1 91 592 60 1063 0.6 1 131 932 61 1315 0.6 1 175 1140 62 1719 0.6 1 190 1529 63 1737 0.6 1 234 1503 64 813 0.6 1 99 714 65 445 0.6 1 41 404 66 1096 0.6 1 175 921 67 642 0.6 1 85 557 68 735 0.6 1 68 667 69 660 0.6 1 85 575 70 685 0.6 1 75 610 71 598 0.6 1 77 521 72 581 0.6 1 78 503 73 556 0.6 1 75 481 74 606 0.6 1 88 518 75 1337 0.6 1 200 1137 76 1069 0.6 1 133 936 77 622 0.6 1 66 556 78 527 0.6 1 56 471 79 552 0.6 1 86 466 80 528 0.6 1 61 467 81 531 0.6 1 67 464 82 537 0.6 1 63 474 83 573 0.6 1 76 497 84 741 0.6 1 99 642 85 618 0.6 1 76 542 86 451 0.6 1 60 391 87 348 0.6 1 31 317 88 319 0.6 1 39 280 89 350 0.6 1 35 315 90 264 0.6 1 31 233 91 257 0.6 1 32 225 92 249 0.6 1 28 221 93 318 0.6 1 42 276 94 354 0.6 1 55 299 95 191 0.6 1 29 162 96 202 0.6 1 29 173 97 241 0.6 1 33 208 98 170 0.6 1 28 142 99 246 0.6 1 34 212 100 215 0.6 1 26 189 101 176 0.6 1 23 153 102 271 0.6 1 35 236 103 109 0.6 1 10 99 104 67 0.6 1 7 60 105 73 0.6 1 8 65 106 54 0.6 1 5 49 107 45 0.6 1 6 39 108 34 0.6 1 4 30 109 80 0.6 1 15 65 110 35 0.6 1 8 27 111 12 0.6 1 3 9 112 2 0.6 1 0 2 113 1 0.6 1 0 1 114 1 0.6 1 0 1 115 1 0.6 1 0 1 116 1 0.6 1 0 1 117 1 0.6 1 0 1 119 1 0.6 1 0 1 121 1 0.6 1 0 1 124 1 0.6 1 1 126 2 0.6 1 1 1 128 1 0.6 1 1 130 1 0.6 1 1 131 1 0.6 1 1 132 3 0.6 1 2 1 133 2 0.6 1 2 134 4 0.6 1 2 2 135 6 0.6 1 6 136 26 0.6 1 23 3 137 444 0.6 1 433 11 138 17053 0.6 1 16710 343 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041626_val_2.fq.gz ============================================= 40788920 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1897252 (4.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 40788920 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 112506 (0.28%)