SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040875_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/77c42ccc-d1de-11eb-b5c3-6c92bfc1303a/trimmed/RRBS20A040875_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 4113.07 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 113,389,968 Reads with adapters: 46,293,855 (40.8%) Reads written (passing filters): 113,389,968 (100.0%) Total basepairs processed: 9,832,846,111 bp Total written (filtered): 8,960,986,277 bp (91.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46293855 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.3% C: 7.9% G: 24.9% T: 37.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 30221808 28347492.0 0 30221808 2 7328235 7086873.0 0 7328235 3 1736935 1771718.2 0 1736935 4 476851 442929.6 0 476851 5 31010 110732.4 0 31010 6 12086 27683.1 0 12086 7 15784 6920.8 0 15784 8 9503 1730.2 0 9503 9 17742 432.5 0 16495 1247 10 13618 108.1 1 5872 7746 11 13007 27.0 1 2078 10929 12 3898 6.8 1 616 3282 13 3661 1.7 1 520 3141 14 12426 1.7 1 1855 10571 15 7295 1.7 1 1247 6048 16 32972 1.7 1 5044 27928 17 31293 1.7 1 6066 25227 18 13176 1.7 1 6025 7151 19 461 1.7 1 78 383 20 4422 1.7 1 726 3696 21 434 1.7 1 88 346 22 847 1.7 1 165 682 23 5058 1.7 1 855 4203 24 24609 1.7 1 4720 19889 25 7942 1.7 1 1475 6467 26 2291 1.7 1 346 1945 27 5924 1.7 1 1023 4901 28 13459 1.7 1 2168 11291 29 16712 1.7 1 2759 13953 30 2533 1.7 1 436 2097 31 478 1.7 1 43 435 32 5126 1.7 1 914 4212 33 21211 1.7 1 3592 17619 34 13221 1.7 1 2231 10990 35 2397 1.7 1 383 2014 36 11093 1.7 1 1949 9144 37 3417 1.7 1 453 2964 38 34343 1.7 1 5165 29178 39 15622 1.7 1 2532 13090 40 4217 1.7 1 633 3584 41 27290 1.7 1 4656 22634 42 2270 1.7 1 250 2020 43 36598 1.7 1 5679 30919 44 6132 1.7 1 956 5176 45 11712 1.7 1 1973 9739 46 2982 1.7 1 418 2564 47 7020 1.7 1 1019 6001 48 20132 1.7 1 3575 16557 49 2830 1.7 1 393 2437 50 9217 1.7 1 1477 7740 51 5315 1.7 1 930 4385 52 2799 1.7 1 444 2355 53 5227 1.7 1 771 4456 54 16726 1.7 1 2694 14032 55 11235 1.7 1 2064 9171 56 7559 1.7 1 1376 6183 57 7791 1.7 1 1308 6483 58 5774 1.7 1 1058 4716 59 5009 1.7 1 956 4053 60 5614 1.7 1 1030 4584 61 9034 1.7 1 1618 7416 62 28636 1.7 1 5919 22717 63 4822 1.7 1 825 3997 64 728 1.7 1 102 626 65 590 1.7 1 70 520 66 5436 1.7 1 958 4478 67 3848 1.7 1 570 3278 68 13389 1.7 1 2353 11036 69 13154 1.7 1 1872 11282 70 19436 1.7 1 2690 16746 71 5509 1.7 1 784 4725 72 2346 1.7 1 362 1984 73 2815 1.7 1 367 2448 74 3914 1.7 1 525 3389 75 5009 1.7 1 618 4391 76 5229 1.7 1 432 4797 77 5966 1.7 1 670 5296 78 8638 1.7 1 1113 7525 79 3624 1.7 1 325 3299 80 3779 1.7 1 305 3474 81 3854 1.7 1 355 3499 82 6074 1.7 1 550 5524 83 5512 1.7 1 505 5007 84 3967 1.7 1 263 3704 85 7335 1.7 1 770 6565 86 4157 1.7 1 311 3846 87 3073 1.7 1 206 2867 88 3283 1.7 1 345 2938 89 4042 1.7 1 336 3706 90 3135 1.7 1 282 2853 91 4183 1.7 1 446 3737 92 2607 1.7 1 219 2388 93 6000 1.7 1 780 5220 94 13125 1.7 1 1242 11883 95 4586 1.7 1 520 4066 96 3311 1.7 1 561 2750 97 8074 1.7 1 1081 6993 98 3715 1.7 1 601 3114 99 1977 1.7 1 275 1702 100 2075 1.7 1 228 1847 101 2546 1.7 1 415 2131 102 3418 1.7 1 618 2800 103 1643 1.7 1 222 1421 104 1227 1.7 1 182 1045 105 1177 1.7 1 192 985 106 1349 1.7 1 220 1129 107 718 1.7 1 78 640 108 473 1.7 1 103 370 109 418 1.7 1 84 334 110 1583 1.7 1 186 1397 111 577 1.7 1 78 499 112 101 1.7 1 22 79 113 24 1.7 1 20 4 114 29 1.7 1 15 14 115 25 1.7 1 19 6 116 32 1.7 1 26 6 117 19 1.7 1 15 4 118 27 1.7 1 23 4 119 18 1.7 1 15 3 120 23 1.7 1 17 6 121 23 1.7 1 15 8 122 26 1.7 1 19 7 123 34 1.7 1 29 5 124 68 1.7 1 53 15 125 59 1.7 1 51 8 126 65 1.7 1 53 12 127 125 1.7 1 93 32 128 106 1.7 1 90 16 129 138 1.7 1 114 24 130 157 1.7 1 130 27 131 229 1.7 1 197 32 132 344 1.7 1 290 54 133 653 1.7 1 552 101 134 975 1.7 1 827 148 135 1807 1.7 1 1600 207 136 3563 1.7 1 3018 545 137 48213 1.7 1 45765 2448 138 5605478 1.7 1 5455414 150064 139 5 1.7 1 2 3 140 22 1.7 1 0 22 143 2 1.7 1 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040875_val_1.fq.gz ============================================= 113389968 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4530777 (4.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 46293847 (40.8%)