SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041626_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/599d18b8-48bc-11eb-aad8-6c92bfbea1ec/trimmed/RRBS20A041626_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 906.23 s (22 us/read; 2.70 M reads/minute). === Summary === Total reads processed: 40,788,920 Reads with adapters: 16,854,972 (41.3%) Reads written (passing filters): 40,788,920 (100.0%) Total basepairs processed: 4,110,531,866 bp Total written (filtered): 4,076,627,815 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16854972 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 0.7% G: 20.6% T: 48.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12239404 10197230.0 0 12239404 2 3412809 2549307.5 0 3412809 3 786370 637326.9 0 786370 4 172649 159331.7 0 172649 5 11043 39832.9 0 11043 6 7156 9958.2 0 7156 7 5070 2489.6 0 5070 8 5490 622.4 0 5490 9 5946 155.6 0 5410 536 10 6743 38.9 1 3395 3348 11 4016 9.7 1 652 3364 12 1797 2.4 1 296 1501 13 1794 0.6 1 301 1493 14 2990 0.6 1 430 2560 15 3004 0.6 1 483 2521 16 5068 0.6 1 697 4371 17 8773 0.6 1 1377 7396 18 3743 0.6 1 752 2991 19 190 0.6 1 23 167 20 1805 0.6 1 368 1437 21 162 0.6 1 17 145 22 287 0.6 1 33 254 23 1493 0.6 1 234 1259 24 4407 0.6 1 764 3643 25 2042 0.6 1 372 1670 26 467 0.6 1 64 403 27 2170 0.6 1 332 1838 28 4467 0.6 1 813 3654 29 4277 0.6 1 833 3444 30 1324 0.6 1 244 1080 31 187 0.6 1 31 156 32 2148 0.6 1 429 1719 33 2721 0.6 1 521 2200 34 2738 0.6 1 571 2167 35 3774 0.6 1 681 3093 36 1309 0.6 1 225 1084 37 1417 0.6 1 230 1187 38 2528 0.6 1 372 2156 39 2302 0.6 1 335 1967 40 1269 0.6 1 219 1050 41 3607 0.6 1 514 3093 42 2685 0.6 1 397 2288 43 11517 0.6 1 1894 9623 44 1841 0.6 1 250 1591 45 2985 0.6 1 508 2477 46 922 0.6 1 129 793 47 1450 0.6 1 205 1245 48 4313 0.6 1 730 3583 49 447 0.6 1 54 393 50 2115 0.6 1 343 1772 51 717 0.6 1 103 614 52 543 0.6 1 81 462 53 1637 0.6 1 276 1361 54 5557 0.6 1 879 4678 55 3382 0.6 1 594 2788 56 1305 0.6 1 199 1106 57 2536 0.6 1 470 2066 58 1514 0.6 1 240 1274 59 620 0.6 1 78 542 60 1292 0.6 1 225 1067 61 1692 0.6 1 261 1431 62 5318 0.6 1 1098 4220 63 1285 0.6 1 228 1057 64 152 0.6 1 23 129 65 148 0.6 1 28 120 66 882 0.6 1 156 726 67 567 0.6 1 72 495 68 2093 0.6 1 312 1781 69 2427 0.6 1 371 2056 70 3859 0.6 1 601 3258 71 1337 0.6 1 196 1141 72 552 0.6 1 74 478 73 903 0.6 1 138 765 74 881 0.6 1 140 741 75 1077 0.6 1 183 894 76 1034 0.6 1 173 861 77 1165 0.6 1 178 987 78 1039 0.6 1 133 906 79 1042 0.6 1 174 868 80 1764 0.6 1 278 1486 81 984 0.6 1 144 840 82 1221 0.6 1 191 1030 83 1161 0.6 1 211 950 84 934 0.6 1 137 797 85 1016 0.6 1 151 865 86 1244 0.6 1 184 1060 87 750 0.6 1 126 624 88 631 0.6 1 93 538 89 893 0.6 1 149 744 90 677 0.6 1 120 557 91 602 0.6 1 91 511 92 630 0.6 1 98 532 93 3542 0.6 1 576 2966 94 4489 0.6 1 687 3802 95 1258 0.6 1 163 1095 96 605 0.6 1 90 515 97 5725 0.6 1 928 4797 98 598 0.6 1 124 474 99 351 0.6 1 63 288 100 315 0.6 1 42 273 101 349 0.6 1 60 289 102 827 0.6 1 170 657 103 207 0.6 1 33 174 104 134 0.6 1 17 117 105 133 0.6 1 18 115 106 168 0.6 1 28 140 107 88 0.6 1 25 63 108 37 0.6 1 5 32 109 44 0.6 1 10 34 110 97 0.6 1 17 80 111 18 0.6 1 5 13 112 3 0.6 1 1 2 113 1 0.6 1 0 1 114 4 0.6 1 0 4 117 3 0.6 1 0 3 119 1 0.6 1 0 1 120 2 0.6 1 0 2 121 1 0.6 1 0 1 124 1 0.6 1 1 128 2 0.6 1 2 132 6 0.6 1 1 5 133 33 0.6 1 6 27 134 12 0.6 1 8 4 135 13 0.6 1 12 1 136 17 0.6 1 11 6 137 427 0.6 1 409 18 138 17159 0.6 1 16795 364 139 1 0.6 1 0 1 140 7 0.6 1 0 7 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041626_val_1.fq.gz ============================================= 40788920 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1577702 (3.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16854972 (41.3%)