SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041520_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/20201115/tmp/44eb47b0-3e8e-11eb-b3f9-b4055d0383c6/trimmed/RRBS20A041520_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1069.20 s (23 us/read; 2.59 M reads/minute). === Summary === Total reads processed: 46,233,883 Reads with adapters: 19,033,630 (41.2%) Reads written (passing filters): 46,233,883 (100.0%) Total basepairs processed: 4,737,180,917 bp Total written (filtered): 4,684,361,108 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19033630 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.5% C: 0.6% G: 20.0% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13740974 11558470.8 0 13740974 2 3855034 2889617.7 0 3855034 3 917305 722404.4 0 917305 4 190211 180601.1 0 190211 5 10777 45150.3 0 10777 6 5955 11287.6 0 5955 7 3496 2821.9 0 3496 8 3229 705.5 0 3229 9 4226 176.4 0 3696 530 10 5740 44.1 1 2085 3655 11 3625 11.0 1 341 3284 12 1546 2.8 1 157 1389 13 1249 0.7 1 150 1099 14 2900 0.7 1 340 2560 15 2213 0.7 1 208 2005 16 5203 0.7 1 443 4760 17 6847 0.7 1 653 6194 18 2633 0.7 1 416 2217 19 151 0.7 1 15 136 20 1275 0.7 1 137 1138 21 152 0.7 1 5 147 22 187 0.7 1 13 174 23 1189 0.7 1 124 1065 24 4337 0.7 1 485 3852 25 1730 0.7 1 209 1521 26 527 0.7 1 49 478 27 1759 0.7 1 196 1563 28 3460 0.7 1 320 3140 29 3862 0.7 1 394 3468 30 784 0.7 1 97 687 31 164 0.7 1 9 155 32 1366 0.7 1 120 1246 33 2464 0.7 1 194 2270 34 2468 0.7 1 290 2178 35 4355 0.7 1 431 3924 36 1833 0.7 1 205 1628 37 713 0.7 1 65 648 38 2633 0.7 1 255 2378 39 1103 0.7 1 124 979 40 3856 0.7 1 278 3578 41 2867 0.7 1 267 2600 42 3044 0.7 1 287 2757 43 4196 0.7 1 379 3817 44 738 0.7 1 66 672 45 2098 0.7 1 191 1907 46 630 0.7 1 63 567 47 1177 0.7 1 126 1051 48 4173 0.7 1 411 3762 49 475 0.7 1 38 437 50 1345 0.7 1 114 1231 51 556 0.7 1 58 498 52 486 0.7 1 40 446 53 969 0.7 1 91 878 54 3471 0.7 1 278 3193 55 2446 0.7 1 261 2185 56 1001 0.7 1 102 899 57 1521 0.7 1 155 1366 58 939 0.7 1 101 838 59 436 0.7 1 35 401 60 778 0.7 1 85 693 61 1016 0.7 1 104 912 62 3634 0.7 1 419 3215 63 775 0.7 1 74 701 64 139 0.7 1 15 124 65 124 0.7 1 10 114 66 666 0.7 1 72 594 67 366 0.7 1 22 344 68 1495 0.7 1 131 1364 69 1760 0.7 1 167 1593 70 2902 0.7 1 269 2633 71 917 0.7 1 73 844 72 348 0.7 1 48 300 73 673 0.7 1 70 603 74 658 0.7 1 56 602 75 891 0.7 1 89 802 76 981 0.7 1 120 861 77 1151 0.7 1 113 1038 78 1053 0.7 1 95 958 79 983 0.7 1 97 886 80 1483 0.7 1 114 1369 81 971 0.7 1 74 897 82 1074 0.7 1 69 1005 83 1235 0.7 1 151 1084 84 911 0.7 1 71 840 85 976 0.7 1 101 875 86 984 0.7 1 81 903 87 673 0.7 1 50 623 88 622 0.7 1 47 575 89 897 0.7 1 83 814 90 776 0.7 1 79 697 91 676 0.7 1 65 611 92 592 0.7 1 47 545 93 3138 0.7 1 179 2959 94 4971 0.7 1 253 4718 95 894 0.7 1 57 837 96 570 0.7 1 57 513 97 5279 0.7 1 271 5008 98 601 0.7 1 42 559 99 322 0.7 1 32 290 100 364 0.7 1 28 336 101 410 0.7 1 45 365 102 1007 0.7 1 118 889 103 244 0.7 1 27 217 104 156 0.7 1 22 134 105 139 0.7 1 16 123 106 149 0.7 1 17 132 107 69 0.7 1 6 63 108 50 0.7 1 7 43 109 48 0.7 1 3 45 110 96 0.7 1 5 91 111 38 0.7 1 1 37 112 8 0.7 1 1 7 113 1 0.7 1 0 1 114 1 0.7 1 0 1 116 1 0.7 1 0 1 117 1 0.7 1 1 118 3 0.7 1 3 119 1 0.7 1 1 121 2 0.7 1 1 1 122 1 0.7 1 1 123 3 0.7 1 2 1 124 3 0.7 1 2 1 125 2 0.7 1 1 1 126 2 0.7 1 1 1 129 1 0.7 1 1 130 3 0.7 1 1 2 131 6 0.7 1 5 1 132 14 0.7 1 6 8 133 56 0.7 1 19 37 134 52 0.7 1 41 11 135 50 0.7 1 33 17 136 62 0.7 1 48 14 137 2224 0.7 1 2112 112 138 143298 0.7 1 139211 4087 140 11 0.7 1 0 11 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041520_val_1.fq.gz ============================================= 46233883 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1855108 (4.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 19033627 (41.2%)