SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000231_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/429dfac2-e7c4-11eb-b765-6c92bfc39756/trimmed/RRBS21T000231_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 868.26 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 44,418,673 Reads with adapters: 17,091,589 (38.5%) Reads written (passing filters): 44,418,673 (100.0%) Total basepairs processed: 3,952,711,478 bp Total written (filtered): 3,787,184,015 bp (95.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17091589 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 8.3% G: 22.3% T: 38.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11567237 11104668.2 0 11567237 2 3151172 2776167.1 0 3151172 3 844461 694041.8 0 844461 4 241269 173510.4 0 241269 5 12588 43377.6 0 12588 6 7774 10844.4 0 7774 7 9940 2711.1 0 9940 8 7093 677.8 0 7093 9 9763 169.4 0 9283 480 10 9636 42.4 1 4927 4709 11 6040 10.6 1 1047 4993 12 2757 2.6 1 530 2227 13 2769 0.7 1 496 2273 14 6186 0.7 1 1012 5174 15 3671 0.7 1 608 3063 16 14176 0.7 1 2245 11931 17 13501 0.7 1 2269 11232 18 5830 0.7 1 1149 4681 19 296 0.7 1 32 264 20 2445 0.7 1 456 1989 21 225 0.7 1 23 202 22 646 0.7 1 87 559 23 2424 0.7 1 434 1990 24 10827 0.7 1 1962 8865 25 4414 0.7 1 807 3607 26 891 0.7 1 116 775 27 3508 0.7 1 604 2904 28 7328 0.7 1 1165 6163 29 8479 0.7 1 1327 7152 30 2311 0.7 1 399 1912 31 726 0.7 1 79 647 32 3406 0.7 1 522 2884 33 7390 0.7 1 1121 6269 34 9360 0.7 1 1545 7815 35 4289 0.7 1 688 3601 36 3666 0.7 1 627 3039 37 7518 0.7 1 1161 6357 38 1338 0.7 1 182 1156 39 1270 0.7 1 215 1055 40 5602 0.7 1 798 4804 41 3485 0.7 1 583 2902 42 6255 0.7 1 987 5268 43 11334 0.7 1 1881 9453 44 1494 0.7 1 178 1316 45 4077 0.7 1 650 3427 46 1216 0.7 1 180 1036 47 2326 0.7 1 317 2009 48 8558 0.7 1 1483 7075 49 690 0.7 1 80 610 50 3115 0.7 1 476 2639 51 1017 0.7 1 122 895 52 823 0.7 1 113 710 53 2273 0.7 1 312 1961 54 5729 0.7 1 882 4847 55 5632 0.7 1 900 4732 56 2465 0.7 1 306 2159 57 2760 0.7 1 422 2338 58 1428 0.7 1 195 1233 59 747 0.7 1 86 661 60 1495 0.7 1 188 1307 61 1766 0.7 1 201 1565 62 8666 0.7 1 1349 7317 63 1716 0.7 1 252 1464 64 266 0.7 1 36 230 65 203 0.7 1 20 183 66 2036 0.7 1 266 1770 67 599 0.7 1 78 521 68 2899 0.7 1 465 2434 69 3601 0.7 1 513 3088 70 4755 0.7 1 723 4032 71 1176 0.7 1 131 1045 72 556 0.7 1 66 490 73 1313 0.7 1 162 1151 74 1436 0.7 1 211 1225 75 1641 0.7 1 242 1399 76 1676 0.7 1 219 1457 77 1940 0.7 1 304 1636 78 2147 0.7 1 317 1830 79 1670 0.7 1 267 1403 80 1525 0.7 1 187 1338 81 1328 0.7 1 174 1154 82 1473 0.7 1 219 1254 83 1544 0.7 1 237 1307 84 1326 0.7 1 182 1144 85 2019 0.7 1 332 1687 86 1067 0.7 1 151 916 87 880 0.7 1 98 782 88 788 0.7 1 105 683 89 926 0.7 1 118 808 90 813 0.7 1 123 690 91 875 0.7 1 125 750 92 650 0.7 1 89 561 93 887 0.7 1 133 754 94 1765 0.7 1 215 1550 95 648 0.7 1 81 567 96 459 0.7 1 52 407 97 804 0.7 1 104 700 98 439 0.7 1 72 367 99 295 0.7 1 37 258 100 310 0.7 1 42 268 101 248 0.7 1 39 209 102 349 0.7 1 55 294 103 206 0.7 1 27 179 104 162 0.7 1 23 139 105 145 0.7 1 17 128 106 137 0.7 1 22 115 107 97 0.7 1 14 83 108 57 0.7 1 7 50 109 64 0.7 1 9 55 110 78 0.7 1 17 61 111 53 0.7 1 7 46 112 26 0.7 1 2 24 113 4 0.7 1 1 3 114 18 0.7 1 4 14 115 4 0.7 1 4 116 1 0.7 1 0 1 117 6 0.7 1 4 2 118 2 0.7 1 1 1 119 5 0.7 1 4 1 120 7 0.7 1 5 2 121 4 0.7 1 4 122 14 0.7 1 14 123 12 0.7 1 11 1 124 7 0.7 1 7 125 22 0.7 1 21 1 126 22 0.7 1 17 5 127 14 0.7 1 11 3 128 18 0.7 1 15 3 129 24 0.7 1 20 4 130 73 0.7 1 67 6 131 76 0.7 1 66 10 132 67 0.7 1 59 8 133 189 0.7 1 169 20 134 482 0.7 1 439 43 135 595 0.7 1 545 50 136 619 0.7 1 549 70 137 15220 0.7 1 14474 746 138 940387 0.7 1 906776 33611 139 4 0.7 1 1 3 140 47 0.7 1 5 42 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000231_val_1.fq.gz ============================================= 44418673 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1563762 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 17091582 (38.5%)