SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041688_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/4b3c370a-3e8e-11eb-9c84-6c92bfc128e4/trimmed/RRBS20A041688_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 951.67 s (24 us/read; 2.50 M reads/minute). === Summary === Total reads processed: 39,575,012 Reads with adapters: 18,069,969 (45.7%) Reads written (passing filters): 39,575,012 (100.0%) Total basepairs processed: 4,189,943,495 bp Total written (filtered): 4,078,974,544 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18069969 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.5% C: 0.9% G: 22.0% T: 45.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12789724 9893753.0 0 12789724 2 3253821 2473438.2 0 3253821 3 955427 618359.6 0 955427 4 196514 154589.9 0 196514 5 23073 38647.5 0 23073 6 13768 9661.9 0 13768 7 13170 2415.5 0 13170 8 12548 603.9 0 12548 9 14452 151.0 0 13681 771 10 13250 37.7 1 8893 4357 11 6853 9.4 1 957 5896 12 2343 2.4 1 423 1920 13 2541 0.6 1 476 2065 14 4103 0.6 1 543 3560 15 3200 0.6 1 505 2695 16 8370 0.6 1 1360 7010 17 11458 0.6 1 2706 8752 18 7618 0.6 1 3777 3841 19 247 0.6 1 34 213 20 2467 0.6 1 470 1997 21 128 0.6 1 5 123 22 269 0.6 1 35 234 23 2196 0.6 1 330 1866 24 7297 0.6 1 1291 6006 25 3152 0.6 1 683 2469 26 788 0.6 1 79 709 27 3170 0.6 1 542 2628 28 5725 0.6 1 891 4834 29 6248 0.6 1 994 5254 30 1468 0.6 1 283 1185 31 260 0.6 1 28 232 32 2351 0.6 1 376 1975 33 3807 0.6 1 548 3259 34 3870 0.6 1 784 3086 35 6707 0.6 1 1208 5499 36 2612 0.6 1 459 2153 37 1259 0.6 1 231 1028 38 4682 0.6 1 810 3872 39 1703 0.6 1 305 1398 40 6534 0.6 1 984 5550 41 4293 0.6 1 773 3520 42 3924 0.6 1 643 3281 43 7142 0.6 1 1155 5987 44 1104 0.6 1 141 963 45 3782 0.6 1 642 3140 46 929 0.6 1 116 813 47 2336 0.6 1 385 1951 48 6743 0.6 1 1170 5573 49 631 0.6 1 74 557 50 2679 0.6 1 426 2253 51 923 0.6 1 152 771 52 576 0.6 1 76 500 53 1713 0.6 1 251 1462 54 4766 0.6 1 755 4011 55 3079 0.6 1 565 2514 56 1690 0.6 1 249 1441 57 2335 0.6 1 420 1915 58 1160 0.6 1 187 973 59 642 0.6 1 67 575 60 1237 0.6 1 190 1047 61 1227 0.6 1 148 1079 62 3900 0.6 1 659 3241 63 1219 0.6 1 216 1003 64 115 0.6 1 21 94 65 69 0.6 1 9 60 66 436 0.6 1 64 372 67 496 0.6 1 50 446 68 2553 0.6 1 426 2127 69 2745 0.6 1 452 2293 70 5092 0.6 1 921 4171 71 1899 0.6 1 295 1604 72 620 0.6 1 74 546 73 737 0.6 1 111 626 74 969 0.6 1 148 821 75 1225 0.6 1 196 1029 76 1689 0.6 1 383 1306 77 1763 0.6 1 333 1430 78 1477 0.6 1 191 1286 79 1399 0.6 1 230 1169 80 1896 0.6 1 311 1585 81 1532 0.6 1 211 1321 82 1803 0.6 1 286 1517 83 1880 0.6 1 359 1521 84 1369 0.6 1 214 1155 85 2089 0.6 1 348 1741 86 1268 0.6 1 213 1055 87 904 0.6 1 124 780 88 835 0.6 1 146 689 89 978 0.6 1 139 839 90 911 0.6 1 163 748 91 793 0.6 1 98 695 92 654 0.6 1 82 572 93 1572 0.6 1 233 1339 94 2650 0.6 1 290 2360 95 924 0.6 1 112 812 96 585 0.6 1 97 488 97 1749 0.6 1 201 1548 98 577 0.6 1 99 478 99 377 0.6 1 58 319 100 405 0.6 1 47 358 101 339 0.6 1 48 291 102 582 0.6 1 101 481 103 255 0.6 1 41 214 104 193 0.6 1 29 164 105 136 0.6 1 14 122 106 127 0.6 1 21 106 107 100 0.6 1 15 85 108 53 0.6 1 1 52 109 53 0.6 1 10 43 110 105 0.6 1 7 98 111 28 0.6 1 6 22 112 7 0.6 1 1 6 114 4 0.6 1 3 1 115 3 0.6 1 0 3 116 7 0.6 1 3 4 117 1 0.6 1 0 1 118 4 0.6 1 3 1 119 2 0.6 1 1 1 120 5 0.6 1 4 1 121 2 0.6 1 2 122 2 0.6 1 2 123 1 0.6 1 0 1 124 4 0.6 1 3 1 125 5 0.6 1 3 2 126 4 0.6 1 1 3 127 7 0.6 1 5 2 128 8 0.6 1 8 129 14 0.6 1 11 3 130 15 0.6 1 14 1 131 15 0.6 1 10 5 132 25 0.6 1 21 4 133 90 0.6 1 64 26 134 135 0.6 1 111 24 135 159 0.6 1 133 26 136 240 0.6 1 201 39 137 6596 0.6 1 6263 333 138 554402 0.6 1 540772 13630 139 1 0.6 1 1 140 2 0.6 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/182021/20201115/RRBS20A041688_val_1.fq.gz ============================================= 39575012 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1244094 (3.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18069966 (45.7%)