SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041587_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/raw_data/cup/BS_workflow/20201121/tmp/c2c95316-3f65-11eb-92b7-6c92bfc12dd0/trimmed/RRBS20A041587_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 662.36 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 26,975,259 Reads with adapters: 11,703,244 (43.4%) Reads written (passing filters): 26,975,259 (100.0%) Total basepairs processed: 2,733,163,634 bp Total written (filtered): 2,638,852,282 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11703244 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 0.6% G: 23.5% T: 46.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8149427 6743814.8 0 8149427 2 2217379 1685953.7 0 2217379 3 526321 421488.4 0 526321 4 115922 105372.1 0 115922 5 9673 26343.0 0 9673 6 4139 6585.8 0 4139 7 3165 1646.4 0 3165 8 3544 411.6 0 3544 9 4225 102.9 0 3873 352 10 4436 25.7 1 2152 2284 11 3386 6.4 1 382 3004 12 1090 1.6 1 182 908 13 1204 0.4 1 161 1043 14 2124 0.4 1 217 1907 15 2234 0.4 1 291 1943 16 3992 0.4 1 594 3398 17 7531 0.4 1 1842 5689 18 5828 0.4 1 3545 2283 19 150 0.4 1 30 120 20 1455 0.4 1 268 1187 21 93 0.4 1 13 80 22 132 0.4 1 21 111 23 1034 0.4 1 129 905 24 2868 0.4 1 436 2432 25 1544 0.4 1 217 1327 26 424 0.4 1 43 381 27 1598 0.4 1 237 1361 28 3328 0.4 1 627 2701 29 3251 0.4 1 526 2725 30 696 0.4 1 120 576 31 169 0.4 1 24 145 32 1295 0.4 1 221 1074 33 1876 0.4 1 283 1593 34 1913 0.4 1 282 1631 35 3442 0.4 1 577 2865 36 1326 0.4 1 198 1128 37 599 0.4 1 144 455 38 2936 0.4 1 789 2147 39 836 0.4 1 112 724 40 3569 0.4 1 458 3111 41 2249 0.4 1 314 1935 42 1858 0.4 1 241 1617 43 4335 0.4 1 581 3754 44 494 0.4 1 56 438 45 2093 0.4 1 294 1799 46 550 0.4 1 76 474 47 1513 0.4 1 190 1323 48 3727 0.4 1 599 3128 49 333 0.4 1 33 300 50 1773 0.4 1 252 1521 51 546 0.4 1 72 474 52 313 0.4 1 37 276 53 1152 0.4 1 172 980 54 3899 0.4 1 511 3388 55 1876 0.4 1 270 1606 56 865 0.4 1 110 755 57 1844 0.4 1 294 1550 58 837 0.4 1 117 720 59 423 0.4 1 62 361 60 999 0.4 1 136 863 61 1070 0.4 1 138 932 62 2840 0.4 1 534 2306 63 860 0.4 1 125 735 64 95 0.4 1 15 80 65 85 0.4 1 5 80 66 386 0.4 1 66 320 67 465 0.4 1 62 403 68 1598 0.4 1 244 1354 69 1766 0.4 1 242 1524 70 3251 0.4 1 460 2791 71 1490 0.4 1 164 1326 72 679 0.4 1 71 608 73 440 0.4 1 55 385 74 542 0.4 1 80 462 75 812 0.4 1 132 680 76 986 0.4 1 196 790 77 973 0.4 1 145 828 78 826 0.4 1 105 721 79 748 0.4 1 125 623 80 912 0.4 1 93 819 81 786 0.4 1 92 694 82 1080 0.4 1 140 940 83 1058 0.4 1 152 906 84 830 0.4 1 101 729 85 822 0.4 1 94 728 86 1148 0.4 1 159 989 87 576 0.4 1 81 495 88 527 0.4 1 65 462 89 657 0.4 1 98 559 90 604 0.4 1 114 490 91 420 0.4 1 41 379 92 529 0.4 1 69 460 93 2700 0.4 1 225 2475 94 3335 0.4 1 328 3007 95 828 0.4 1 89 739 96 482 0.4 1 51 431 97 2521 0.4 1 207 2314 98 412 0.4 1 73 339 99 283 0.4 1 40 243 100 322 0.4 1 30 292 101 319 0.4 1 41 278 102 688 0.4 1 92 596 103 187 0.4 1 20 167 104 116 0.4 1 28 88 105 94 0.4 1 11 83 106 147 0.4 1 20 127 107 84 0.4 1 14 70 108 29 0.4 1 3 26 109 27 0.4 1 4 23 110 65 0.4 1 8 57 111 17 0.4 1 5 12 112 10 0.4 1 7 3 113 7 0.4 1 2 5 114 14 0.4 1 4 10 115 9 0.4 1 6 3 116 15 0.4 1 7 8 117 2 0.4 1 2 118 3 0.4 1 3 119 1 0.4 1 0 1 120 3 0.4 1 0 3 121 5 0.4 1 3 2 122 5 0.4 1 3 2 123 7 0.4 1 5 2 124 5 0.4 1 1 4 125 3 0.4 1 3 126 5 0.4 1 4 1 127 11 0.4 1 9 2 128 16 0.4 1 15 1 129 15 0.4 1 13 2 130 31 0.4 1 25 6 131 24 0.4 1 22 2 132 25 0.4 1 21 4 133 90 0.4 1 64 26 134 143 0.4 1 120 23 135 190 0.4 1 166 24 136 303 0.4 1 270 33 137 18607 0.4 1 18051 556 138 509329 0.4 1 497392 11937 139 2 0.4 1 1 1 140 9 0.4 1 3 6 141 1 0.4 1 0 1 143 4 0.4 1 1 3 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041587_val_1.fq.gz ============================================= 26975259 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 935081 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11703230 (43.4%)