SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041586_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/602aec6e-48bc-11eb-9ac6-6c92bfc12d88/trimmed/RRBS20A041586_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 523.14 s (23 us/read; 2.60 M reads/minute). === Summary === Total reads processed: 22,673,732 Reads with adapters: 9,253,298 (40.8%) Reads written (passing filters): 22,673,732 (100.0%) Total basepairs processed: 2,213,485,720 bp Total written (filtered): 2,190,203,604 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9253298 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.5% C: 0.8% G: 21.2% T: 47.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6762278 5668433.0 0 6762278 2 1793745 1417108.2 0 1793745 3 419822 354277.1 0 419822 4 97952 88569.3 0 97952 5 6694 22142.3 0 6694 6 2310 5535.6 0 2310 7 2056 1383.9 0 2056 8 1505 346.0 0 1505 9 2065 86.5 0 1802 263 10 3365 21.6 1 904 2461 11 2084 5.4 1 282 1802 12 1043 1.4 1 136 907 13 1062 0.3 1 179 883 14 1590 0.3 1 183 1407 15 1430 0.3 1 213 1217 16 3143 0.3 1 450 2693 17 4667 0.3 1 735 3932 18 2407 0.3 1 576 1831 19 107 0.3 1 11 96 20 1120 0.3 1 151 969 21 100 0.3 1 18 82 22 201 0.3 1 30 171 23 1212 0.3 1 189 1023 24 2835 0.3 1 522 2313 25 1567 0.3 1 291 1276 26 342 0.3 1 48 294 27 1710 0.3 1 250 1460 28 2751 0.3 1 426 2325 29 2433 0.3 1 357 2076 30 949 0.3 1 153 796 31 127 0.3 1 14 113 32 1421 0.3 1 163 1258 33 2534 0.3 1 397 2137 34 2806 0.3 1 399 2407 35 657 0.3 1 101 556 36 1797 0.3 1 264 1533 37 231 0.3 1 23 208 38 2841 0.3 1 378 2463 39 2516 0.3 1 332 2184 40 940 0.3 1 133 807 41 2925 0.3 1 445 2480 42 317 0.3 1 35 282 43 3199 0.3 1 434 2765 44 593 0.3 1 78 515 45 2044 0.3 1 313 1731 46 690 0.3 1 83 607 47 1483 0.3 1 197 1286 48 3328 0.3 1 451 2877 49 328 0.3 1 33 295 50 1628 0.3 1 210 1418 51 565 0.3 1 79 486 52 513 0.3 1 80 433 53 1663 0.3 1 259 1404 54 3597 0.3 1 593 3004 55 2720 0.3 1 426 2294 56 1253 0.3 1 163 1090 57 2228 0.3 1 353 1875 58 1573 0.3 1 241 1332 59 818 0.3 1 122 696 60 1602 0.3 1 262 1340 61 2206 0.3 1 326 1880 62 5799 0.3 1 1174 4625 63 1279 0.3 1 189 1090 64 185 0.3 1 28 157 65 232 0.3 1 27 205 66 1040 0.3 1 157 883 67 678 0.3 1 85 593 68 1771 0.3 1 241 1530 69 1993 0.3 1 268 1725 70 3366 0.3 1 503 2863 71 1360 0.3 1 163 1197 72 738 0.3 1 107 631 73 847 0.3 1 145 702 74 723 0.3 1 128 595 75 730 0.3 1 102 628 76 779 0.3 1 126 653 77 908 0.3 1 130 778 78 871 0.3 1 99 772 79 789 0.3 1 144 645 80 1274 0.3 1 193 1081 81 872 0.3 1 114 758 82 915 0.3 1 129 786 83 912 0.3 1 134 778 84 934 0.3 1 138 796 85 1209 0.3 1 177 1032 86 770 0.3 1 108 662 87 522 0.3 1 65 457 88 592 0.3 1 71 521 89 677 0.3 1 109 568 90 530 0.3 1 69 461 91 514 0.3 1 59 455 92 509 0.3 1 68 441 93 1289 0.3 1 201 1088 94 2054 0.3 1 341 1713 95 714 0.3 1 114 600 96 425 0.3 1 65 360 97 1752 0.3 1 264 1488 98 454 0.3 1 73 381 99 324 0.3 1 50 274 100 305 0.3 1 31 274 101 359 0.3 1 48 311 102 575 0.3 1 127 448 103 220 0.3 1 38 182 104 132 0.3 1 21 111 105 134 0.3 1 20 114 106 139 0.3 1 35 104 107 97 0.3 1 15 82 108 36 0.3 1 7 29 109 35 0.3 1 9 26 110 93 0.3 1 13 80 111 9 0.3 1 2 7 112 6 0.3 1 3 3 113 2 0.3 1 1 1 114 3 0.3 1 1 2 115 3 0.3 1 0 3 116 1 0.3 1 0 1 120 1 0.3 1 1 122 2 0.3 1 1 1 123 1 0.3 1 1 125 1 0.3 1 1 127 5 0.3 1 3 2 128 3 0.3 1 3 129 5 0.3 1 3 2 130 4 0.3 1 2 2 131 2 0.3 1 1 1 132 14 0.3 1 11 3 133 31 0.3 1 12 19 134 28 0.3 1 23 5 135 30 0.3 1 27 3 136 54 0.3 1 40 14 137 1295 0.3 1 1244 51 138 32649 0.3 1 31735 914 139 3 0.3 1 2 1 140 3 0.3 1 0 3 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041586_val_1.fq.gz ============================================= 22673732 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1234310 (5.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 9253297 (40.8%)