SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041609_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) 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/processing/cup/BS_workflow/20201104_20201106/tmp/5eb97c56-48bc-11eb-b85d-6c92bfc12dee/trimmed/RRBS20A041609_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 342.08 s (22 us/read; 2.75 M reads/minute). === Summary === Total reads processed: 15,695,213 Reads with adapters: 6,498,861 (41.4%) Reads written (passing filters): 15,695,213 (100.0%) Total basepairs processed: 1,506,153,551 bp Total written (filtered): 1,493,001,254 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6498861 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.9% C: 74.4% G: 1.8% T: 5.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6369257 3923803.2 0 6369257 2 42472 980950.8 0 42472 3 5574 245237.7 0 5574 4 3643 61309.4 0 3643 5 1361 15327.4 0 1361 6 574 3831.8 0 574 7 1150 958.0 0 1150 8 594 239.5 0 594 9 326 59.9 0 294 32 10 2509 15.0 1 644 1865 11 98 3.7 1 8 90 12 1972 0.9 1 441 1531 13 523 0.2 1 62 461 14 719 0.2 1 91 628 15 274 0.2 1 32 242 16 315 0.2 1 33 282 17 598 0.2 1 56 542 18 224 0.2 1 13 211 19 653 0.2 1 51 602 20 464 0.2 1 43 421 21 30 0.2 1 1 29 22 411 0.2 1 55 356 23 575 0.2 1 50 525 24 1536 0.2 1 153 1383 25 492 0.2 1 33 459 26 892 0.2 1 94 798 27 334 0.2 1 36 298 28 593 0.2 1 69 524 29 61 0.2 1 5 56 30 501 0.2 1 51 450 31 427 0.2 1 36 391 32 507 0.2 1 44 463 33 1349 0.2 1 156 1193 34 490 0.2 1 49 441 35 572 0.2 1 48 524 36 129 0.2 1 8 121 37 748 0.2 1 95 653 38 220 0.2 1 12 208 39 236 0.2 1 25 211 40 204 0.2 1 17 187 41 317 0.2 1 35 282 42 513 0.2 1 60 453 43 277 0.2 1 35 242 44 382 0.2 1 36 346 45 796 0.2 1 76 720 46 415 0.2 1 39 376 47 128 0.2 1 11 117 48 566 0.2 1 49 517 49 366 0.2 1 36 330 50 645 0.2 1 64 581 51 563 0.2 1 51 512 52 516 0.2 1 43 473 53 77 0.2 1 8 69 54 377 0.2 1 48 329 55 285 0.2 1 25 260 56 66 0.2 1 4 62 57 248 0.2 1 22 226 58 617 0.2 1 50 567 59 281 0.2 1 32 249 60 495 0.2 1 40 455 61 584 0.2 1 63 521 62 772 0.2 1 89 683 63 704 0.2 1 63 641 64 263 0.2 1 31 232 65 186 0.2 1 14 172 66 421 0.2 1 49 372 67 366 0.2 1 52 314 68 343 0.2 1 31 312 69 300 0.2 1 43 257 70 302 0.2 1 25 277 71 305 0.2 1 27 278 72 311 0.2 1 25 286 73 255 0.2 1 30 225 74 300 0.2 1 37 263 75 477 0.2 1 53 424 76 457 0.2 1 44 413 77 431 0.2 1 23 408 78 290 0.2 1 23 267 79 291 0.2 1 20 271 80 267 0.2 1 29 238 81 213 0.2 1 14 199 82 241 0.2 1 25 216 83 263 0.2 1 26 237 84 296 0.2 1 33 263 85 245 0.2 1 28 217 86 216 0.2 1 26 190 87 149 0.2 1 16 133 88 180 0.2 1 13 167 89 178 0.2 1 16 162 90 167 0.2 1 14 153 91 132 0.2 1 14 118 92 141 0.2 1 11 130 93 155 0.2 1 17 138 94 161 0.2 1 25 136 95 82 0.2 1 10 72 96 104 0.2 1 11 93 97 103 0.2 1 14 89 98 74 0.2 1 6 68 99 84 0.2 1 9 75 100 80 0.2 1 9 71 101 53 0.2 1 8 45 102 54 0.2 1 4 50 103 56 0.2 1 10 46 104 26 0.2 1 1 25 105 25 0.2 1 3 22 106 28 0.2 1 1 27 107 16 0.2 1 4 12 108 15 0.2 1 1 14 109 18 0.2 1 0 18 110 36 0.2 1 8 28 111 1 0.2 1 0 1 112 1 0.2 1 0 1 116 3 0.2 1 0 3 117 2 0.2 1 1 1 123 3 0.2 1 3 124 1 0.2 1 1 126 2 0.2 1 1 1 128 5 0.2 1 5 129 3 0.2 1 2 1 130 2 0.2 1 2 131 1 0.2 1 1 132 2 0.2 1 1 1 133 7 0.2 1 6 1 134 6 0.2 1 5 1 135 21 0.2 1 20 1 136 92 0.2 1 87 5 137 9218 0.2 1 9073 145 138 26738 0.2 1 26369 369 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041609_val_2.fq.gz ============================================= 15695213 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 718696 (4.6%) 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: 15695213 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 86642 (0.55%)