SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000220_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) 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/test_BSworkflow/test_analysis_2/tmp/429273a0-e7c4-11eb-ad2f-6c92bfc12dd0/trimmed/RRBS21T000220_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1555.17 s (18 us/read; 3.40 M reads/minute). === Summary === Total reads processed: 88,179,496 Reads with adapters: 37,465,255 (42.5%) Reads written (passing filters): 88,179,496 (100.0%) Total basepairs processed: 7,260,332,959 bp Total written (filtered): 6,945,450,841 bp (95.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 37465255 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.4% C: 0.5% G: 30.9% T: 35.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25728895 22044874.0 0 25728895 2 6158135 5511218.5 0 6158135 3 2414306 1377804.6 0 2414306 4 697514 344451.2 0 697514 5 23404 86112.8 0 23404 6 11119 21528.2 0 11119 7 13099 5382.0 0 13099 8 8815 1345.5 0 8815 9 15103 336.4 0 13757 1346 10 13345 84.1 1 5199 8146 11 13668 21.0 1 1840 11828 12 3859 5.3 1 559 3300 13 4339 1.3 1 602 3737 14 11589 1.3 1 1743 9846 15 6452 1.3 1 904 5548 16 26900 1.3 1 3696 23204 17 22630 1.3 1 3362 19268 18 9929 1.3 1 2646 7283 19 370 1.3 1 42 328 20 5197 1.3 1 895 4302 21 365 1.3 1 50 315 22 923 1.3 1 139 784 23 5133 1.3 1 745 4388 24 24844 1.3 1 3646 21198 25 9394 1.3 1 1430 7964 26 2475 1.3 1 351 2124 27 6771 1.3 1 942 5829 28 15258 1.3 1 2257 13001 29 17848 1.3 1 2625 15223 30 3633 1.3 1 510 3123 31 513 1.3 1 42 471 32 5261 1.3 1 729 4532 33 11606 1.3 1 1597 10009 34 12888 1.3 1 1879 11009 35 25482 1.3 1 3710 21772 36 5140 1.3 1 783 4357 37 2588 1.3 1 350 2238 38 15328 1.3 1 2273 13055 39 13176 1.3 1 2220 10956 40 2406 1.3 1 268 2138 41 35113 1.3 1 5495 29618 42 4431 1.3 1 617 3814 43 36884 1.3 1 5887 30997 44 5919 1.3 1 868 5051 45 10062 1.3 1 1552 8510 46 2546 1.3 1 389 2157 47 5120 1.3 1 711 4409 48 19502 1.3 1 3182 16320 49 1716 1.3 1 246 1470 50 10815 1.3 1 1738 9077 51 3839 1.3 1 595 3244 52 1996 1.3 1 275 1721 53 5897 1.3 1 797 5100 54 15042 1.3 1 2441 12601 55 12560 1.3 1 2145 10415 56 6269 1.3 1 968 5301 57 7966 1.3 1 1318 6648 58 3428 1.3 1 475 2953 59 2818 1.3 1 408 2410 60 4694 1.3 1 754 3940 61 4900 1.3 1 673 4227 62 28093 1.3 1 4922 23171 63 5738 1.3 1 923 4815 64 597 1.3 1 73 524 65 351 1.3 1 43 308 66 3583 1.3 1 568 3015 67 2055 1.3 1 285 1770 68 8981 1.3 1 1436 7545 69 9728 1.3 1 1495 8233 70 17253 1.3 1 2916 14337 71 4779 1.3 1 721 4058 72 1660 1.3 1 214 1446 73 2315 1.3 1 313 2002 74 3740 1.3 1 578 3162 75 4331 1.3 1 693 3638 76 5141 1.3 1 798 4343 77 6528 1.3 1 994 5534 78 5440 1.3 1 795 4645 79 5199 1.3 1 728 4471 80 4845 1.3 1 716 4129 81 4647 1.3 1 675 3972 82 5732 1.3 1 728 5004 83 6827 1.3 1 1088 5739 84 5214 1.3 1 745 4469 85 7903 1.3 1 1245 6658 86 4481 1.3 1 802 3679 87 3456 1.3 1 513 2943 88 3279 1.3 1 495 2784 89 3095 1.3 1 458 2637 90 2768 1.3 1 402 2366 91 3395 1.3 1 513 2882 92 2888 1.3 1 440 2448 93 3084 1.3 1 430 2654 94 4282 1.3 1 513 3769 95 2603 1.3 1 412 2191 96 2151 1.3 1 281 1870 97 2834 1.3 1 420 2414 98 1994 1.3 1 340 1654 99 1558 1.3 1 232 1326 100 1649 1.3 1 272 1377 101 1113 1.3 1 179 934 102 1228 1.3 1 183 1045 103 1063 1.3 1 164 899 104 624 1.3 1 94 530 105 543 1.3 1 69 474 106 452 1.3 1 84 368 107 344 1.3 1 48 296 108 189 1.3 1 28 161 109 193 1.3 1 24 169 110 193 1.3 1 29 164 111 101 1.3 1 13 88 112 44 1.3 1 2 42 113 6 1.3 1 5 1 114 40 1.3 1 8 32 115 13 1.3 1 1 12 116 15 1.3 1 2 13 117 2 1.3 1 1 1 118 2 1.3 1 2 119 1 1.3 1 1 120 4 1.3 1 3 1 121 7 1.3 1 4 3 122 5 1.3 1 3 2 123 2 1.3 1 2 124 2 1.3 1 1 1 125 3 1.3 1 1 2 126 5 1.3 1 3 2 127 7 1.3 1 2 5 128 9 1.3 1 6 3 129 6 1.3 1 5 1 130 13 1.3 1 10 3 131 21 1.3 1 14 7 132 30 1.3 1 25 5 133 73 1.3 1 52 21 134 178 1.3 1 151 27 135 233 1.3 1 200 33 136 766 1.3 1 444 322 137 53748 1.3 1 51030 2718 138 1638557 1.3 1 1555832 82725 139 3 1.3 1 1 2 140 2 1.3 1 0 2 143 1 1.3 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000220_val_1.fq.gz ============================================= 88179496 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2669678 (3.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 37465252 (42.5%)