SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000236_val_2.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_20210722/tmp/f93fdf04-1990-11ec-8507-6c92bfc12faa/trimmed/RRBS21T000236_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1078.97 s (27 us/read; 2.24 M reads/minute). === Summary === Total reads processed: 40,219,190 Reads with adapters: 27,808,546 (69.1%) Reads written (passing filters): 40,219,190 (100.0%) Total basepairs processed: 4,077,576,661 bp Total written (filtered): 2,075,629,103 bp (50.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27808546 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 54.7% C: 44.2% G: 0.1% T: 1.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13254918 10054797.5 0 13254918 2 93983 2513699.4 0 93983 3 7744 628424.8 0 7744 4 2268 157106.2 0 2268 5 868 39276.6 0 868 6 720 9819.1 0 720 7 1251 2454.8 0 1251 8 692 613.7 0 692 9 328 153.4 0 293 35 10 4090 38.4 1 797 3293 11 136 9.6 1 17 119 12 3242 2.4 1 557 2685 13 681 0.6 1 55 626 14 1108 0.6 1 73 1035 15 306 0.6 1 19 287 16 394 0.6 1 33 361 17 942 0.6 1 58 884 18 345 0.6 1 29 316 19 1868 0.6 1 513 1355 20 738 0.6 1 160 578 21 948 0.6 1 699 249 22 440 0.6 1 54 386 23 783 0.6 1 55 728 24 2190 0.6 1 132 2058 25 760 0.6 1 38 722 26 615 0.6 1 68 547 27 191 0.6 1 49 142 28 537 0.6 1 57 480 29 176 0.6 1 6 170 30 658 0.6 1 53 605 31 424 0.6 1 54 370 32 854 0.6 1 76 778 33 665 0.6 1 72 593 34 375 0.6 1 22 353 35 647 0.6 1 60 587 36 484 0.6 1 35 449 37 412 0.6 1 36 376 38 339 0.6 1 29 310 39 316 0.6 1 22 294 40 314 0.6 1 16 298 41 522 0.6 1 23 499 42 533 0.6 1 32 501 43 396 0.6 1 17 379 44 450 0.6 1 22 428 45 627 0.6 1 37 590 46 362 0.6 1 21 341 47 369 0.6 1 26 343 48 842 0.6 1 62 780 49 555 0.6 1 37 518 50 311 0.6 1 22 289 51 762 0.6 1 49 713 52 907 0.6 1 62 845 53 733 0.6 1 35 698 54 567 0.6 1 45 522 55 530 0.6 1 36 494 56 459 0.6 1 21 438 57 685 0.6 1 33 652 58 386 0.6 1 34 352 59 369 0.6 1 22 347 60 290 0.6 1 23 267 61 242 0.6 1 21 221 62 251 0.6 1 21 230 63 320 0.6 1 37 283 64 307 0.6 1 37 270 65 410 0.6 1 54 356 66 653 0.6 1 50 603 67 451 0.6 1 42 409 68 436 0.6 1 36 400 69 460 0.6 1 32 428 70 462 0.6 1 36 426 71 460 0.6 1 33 427 72 608 0.6 1 57 551 73 482 0.6 1 50 432 74 467 0.6 1 24 443 75 778 0.6 1 56 722 76 970 0.6 1 94 876 77 484 0.6 1 37 447 78 398 0.6 1 25 373 79 376 0.6 1 27 349 80 334 0.6 1 21 313 81 335 0.6 1 14 321 82 238 0.6 1 10 228 83 249 0.6 1 19 230 84 233 0.6 1 8 225 85 211 0.6 1 22 189 86 169 0.6 1 11 158 87 163 0.6 1 15 148 88 143 0.6 1 10 133 89 168 0.6 1 16 152 90 107 0.6 1 7 100 91 157 0.6 1 9 148 92 166 0.6 1 10 156 93 148 0.6 1 13 135 94 108 0.6 1 8 100 95 145 0.6 1 7 138 96 112 0.6 1 8 104 97 133 0.6 1 11 122 98 104 0.6 1 9 95 99 95 0.6 1 7 88 100 103 0.6 1 10 93 101 57 0.6 1 6 51 102 71 0.6 1 6 65 103 70 0.6 1 6 64 104 65 0.6 1 2 63 105 38 0.6 1 7 31 106 29 0.6 1 4 25 107 31 0.6 1 6 25 108 178 0.6 1 25 153 109 72 0.6 1 14 58 110 43 0.6 1 6 37 111 13 0.6 1 5 8 112 10 0.6 1 4 6 113 9 0.6 1 6 3 114 29 0.6 1 2 27 115 26 0.6 1 15 11 116 56 0.6 1 13 43 117 15 0.6 1 12 3 118 23 0.6 1 14 9 119 11 0.6 1 6 5 120 8 0.6 1 8 121 16 0.6 1 13 3 122 19 0.6 1 18 1 123 16 0.6 1 14 2 124 20 0.6 1 17 3 125 30 0.6 1 26 4 126 54 0.6 1 52 2 127 64 0.6 1 58 6 128 107 0.6 1 97 10 129 161 0.6 1 152 9 130 138 0.6 1 127 11 131 166 0.6 1 145 21 132 184 0.6 1 170 14 133 309 0.6 1 287 22 134 565 0.6 1 530 35 135 1674 0.6 1 1537 137 136 4429 0.6 1 4209 220 137 251959 0.6 1 246837 5122 138 14135724 0.6 1 13985463 150261 139 16 0.6 1 0 16 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000236_val_2.fq.gz ============================================= 40219190 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 796515 (2.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 40219190 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 14569848 (36.23%)