SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040773_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 1 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 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/tmp/7739f4e4-d1de-11eb-badf-6c92bfc12bba/trimmed/RRBS20A040773_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1138.11 s (10 us/read; 5.88 M reads/minute). === Summary === Total reads processed: 111,598,811 Reads with adapters: 106,850,629 (95.7%) Reads written (passing filters): 111,598,811 (100.0%) Total basepairs processed: 15,425,729,117 bp Total written (filtered): 1,142,048,737 bp (7.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 106850629 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 1.1% C: 0.0% G: 97.5% T: 1.4% none/other: 0.0% WARNING: The adapter is preceded by "G" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 2417538 27899702.8 0 2417538 2 545440 6974925.7 0 545440 3 148956 1743731.4 0 148956 4 44418 435932.9 0 44418 5 1473 108983.2 0 1473 6 620 27245.8 0 620 7 780 6811.5 0 780 8 631 1702.9 0 631 9 803 425.7 0 707 96 10 576 106.4 1 300 276 11 586 26.6 1 89 497 12 183 6.7 1 43 140 13 304 1.7 1 71 233 14 333 1.7 1 60 273 15 515 1.7 1 86 429 16 3150 1.7 1 291 2859 17 11354 1.7 1 2881 8473 18 43651 1.7 1 20306 23345 19 441 1.7 1 105 336 20 410 1.7 1 73 337 21 545 1.7 1 175 370 22 1596 1.7 1 746 850 23 247 1.7 1 43 204 24 595 1.7 1 103 492 25 290 1.7 1 45 245 26 114 1.7 1 17 97 27 488 1.7 1 128 360 28 721 1.7 1 144 577 29 595 1.7 1 115 480 30 189 1.7 1 51 138 31 58 1.7 1 15 43 32 341 1.7 1 72 269 33 455 1.7 1 89 366 34 638 1.7 1 130 508 35 1240 1.7 1 266 974 36 586 1.7 1 117 469 37 2452 1.7 1 468 1984 38 753 1.7 1 177 576 39 249 1.7 1 58 191 40 1964 1.7 1 523 1441 41 937 1.7 1 277 660 42 420 1.7 1 103 317 43 1932 1.7 1 607 1325 44 569 1.7 1 152 417 45 1018 1.7 1 299 719 46 461 1.7 1 140 321 47 909 1.7 1 297 612 48 2165 1.7 1 629 1536 49 223 1.7 1 62 161 50 911 1.7 1 319 592 51 1505 1.7 1 447 1058 52 523 1.7 1 175 348 53 920 1.7 1 341 579 54 3011 1.7 1 1050 1961 55 1836 1.7 1 737 1099 56 2047 1.7 1 751 1296 57 2296 1.7 1 793 1503 58 3341 1.7 1 1441 1900 59 2408 1.7 1 675 1733 60 3622 1.7 1 1469 2153 61 8991 1.7 1 3186 5805 62 15394 1.7 1 4715 10679 63 1966 1.7 1 885 1081 64 322 1.7 1 108 214 65 604 1.7 1 192 412 66 4531 1.7 1 1264 3267 67 1963 1.7 1 254 1709 68 2375 1.7 1 627 1748 69 2846 1.7 1 1145 1701 70 5566 1.7 1 2976 2590 71 5759 1.7 1 3589 2170 72 9492 1.7 1 6745 2747 73 8064 1.7 1 6382 1682 74 3247 1.7 1 2369 878 75 2209 1.7 1 1450 759 76 2020 1.7 1 1360 660 77 2037 1.7 1 1211 826 78 1973 1.7 1 1277 696 79 2124 1.7 1 1415 709 80 2406 1.7 1 1684 722 81 2314 1.7 1 1708 606 82 2632 1.7 1 1709 923 83 2194 1.7 1 1501 693 84 2735 1.7 1 2021 714 85 2676 1.7 1 1892 784 86 2359 1.7 1 1751 608 87 2287 1.7 1 1598 689 88 1954 1.7 1 1437 517 89 2527 1.7 1 1875 652 90 2550 1.7 1 1881 669 91 2089 1.7 1 1613 476 92 2694 1.7 1 2141 553 93 2276 1.7 1 1750 526 94 2389 1.7 1 1801 588 95 2069 1.7 1 1674 395 96 2467 1.7 1 1964 503 97 2303 1.7 1 1730 573 98 2432 1.7 1 1833 599 99 2425 1.7 1 2023 402 100 2196 1.7 1 1806 390 101 2058 1.7 1 1670 388 102 2806 1.7 1 2377 429 103 2962 1.7 1 2491 471 104 2699 1.7 1 2289 410 105 2738 1.7 1 2338 400 106 3174 1.7 1 2663 511 107 3363 1.7 1 2800 563 108 3016 1.7 1 2442 574 109 3183 1.7 1 2564 619 110 3941 1.7 1 3099 842 111 3714 1.7 1 3105 609 112 3735 1.7 1 3241 494 113 3907 1.7 1 3407 500 114 4462 1.7 1 3855 607 115 5442 1.7 1 4797 645 116 7566 1.7 1 6791 775 117 6597 1.7 1 5839 758 118 6574 1.7 1 5839 735 119 6474 1.7 1 5711 763 120 7137 1.7 1 6303 834 121 9845 1.7 1 8731 1114 122 11151 1.7 1 9930 1221 123 12443 1.7 1 11119 1324 124 15076 1.7 1 13497 1579 125 15820 1.7 1 14130 1690 126 15780 1.7 1 14137 1643 127 22313 1.7 1 20041 2272 128 27674 1.7 1 24789 2885 129 29487 1.7 1 26480 3007 130 27942 1.7 1 24739 3203 131 36018 1.7 1 31888 4130 132 48707 1.7 1 42965 5742 133 103813 1.7 1 93575 10238 134 132463 1.7 1 118876 13587 135 276709 1.7 1 256468 20241 136 481476 1.7 1 453616 27860 137 3085008 1.7 1 2964077 120931 138 98659198 1.7 1 96026984 2632214 139 4079 1.7 1 3530 549 140 351273 1.7 1 338610 12663 141 2 1.7 1 0 2 142 8 1.7 1 3 5 143 7 1.7 1 0 7 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040773_val_1.fq.gz ============================================= 111598811 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 547744 (0.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 106850592 (95.7%)