SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041605_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/5aae55dc-48bc-11eb-8640-6c92bfc12e8a/trimmed/RRBS20A041605_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 315.66 s (23 us/read; 2.64 M reads/minute). === Summary === Total reads processed: 13,870,585 Reads with adapters: 5,573,321 (40.2%) Reads written (passing filters): 13,870,585 (100.0%) Total basepairs processed: 1,378,807,975 bp Total written (filtered): 1,368,875,392 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5573321 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.8% C: 76.1% G: 1.6% T: 5.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5468594 3467646.2 0 5468594 2 39218 866911.6 0 39218 3 5492 216727.9 0 5492 4 3529 54182.0 0 3529 5 1222 13545.5 0 1222 6 547 3386.4 0 547 7 993 846.6 0 993 8 511 211.6 0 511 9 273 52.9 0 244 29 10 2422 13.2 1 557 1865 11 100 3.3 1 12 88 12 1686 0.8 1 373 1313 13 486 0.2 1 48 438 14 685 0.2 1 57 628 15 266 0.2 1 29 237 16 342 0.2 1 33 309 17 746 0.2 1 68 678 18 227 0.2 1 16 211 19 542 0.2 1 43 499 20 440 0.2 1 45 395 21 35 0.2 1 2 33 22 339 0.2 1 28 311 23 465 0.2 1 38 427 24 1320 0.2 1 116 1204 25 473 0.2 1 45 428 26 713 0.2 1 61 652 27 315 0.2 1 28 287 28 487 0.2 1 61 426 29 48 0.2 1 1 47 30 435 0.2 1 42 393 31 415 0.2 1 46 369 32 388 0.2 1 37 351 33 1131 0.2 1 100 1031 34 338 0.2 1 30 308 35 464 0.2 1 37 427 36 101 0.2 1 6 95 37 584 0.2 1 71 513 38 163 0.2 1 13 150 39 224 0.2 1 24 200 40 170 0.2 1 12 158 41 248 0.2 1 23 225 42 434 0.2 1 58 376 43 207 0.2 1 22 185 44 321 0.2 1 31 290 45 661 0.2 1 65 596 46 363 0.2 1 32 331 47 109 0.2 1 10 99 48 452 0.2 1 32 420 49 289 0.2 1 30 259 50 513 0.2 1 50 463 51 465 0.2 1 46 419 52 419 0.2 1 62 357 53 54 0.2 1 3 51 54 349 0.2 1 45 304 55 218 0.2 1 19 199 56 41 0.2 1 5 36 57 183 0.2 1 17 166 58 444 0.2 1 52 392 59 284 0.2 1 28 256 60 357 0.2 1 30 327 61 436 0.2 1 37 399 62 539 0.2 1 55 484 63 483 0.2 1 56 427 64 155 0.2 1 13 142 65 140 0.2 1 10 130 66 313 0.2 1 30 283 67 282 0.2 1 23 259 68 272 0.2 1 21 251 69 234 0.2 1 24 210 70 204 0.2 1 20 184 71 192 0.2 1 13 179 72 233 0.2 1 30 203 73 184 0.2 1 25 159 74 149 0.2 1 8 141 75 380 0.2 1 34 346 76 253 0.2 1 25 228 77 229 0.2 1 15 214 78 170 0.2 1 11 159 79 192 0.2 1 22 170 80 197 0.2 1 18 179 81 158 0.2 1 15 143 82 165 0.2 1 11 154 83 203 0.2 1 29 174 84 170 0.2 1 20 150 85 177 0.2 1 16 161 86 153 0.2 1 13 140 87 123 0.2 1 7 116 88 124 0.2 1 11 113 89 126 0.2 1 13 113 90 105 0.2 1 13 92 91 87 0.2 1 5 82 92 90 0.2 1 9 81 93 113 0.2 1 8 105 94 103 0.2 1 11 92 95 58 0.2 1 8 50 96 66 0.2 1 9 57 97 72 0.2 1 6 66 98 65 0.2 1 4 61 99 53 0.2 1 8 45 100 62 0.2 1 6 56 101 44 0.2 1 3 41 102 54 0.2 1 9 45 103 25 0.2 1 0 25 104 18 0.2 1 0 18 105 11 0.2 1 4 7 106 20 0.2 1 0 20 107 8 0.2 1 0 8 108 7 0.2 1 1 6 109 8 0.2 1 1 7 110 40 0.2 1 7 33 112 1 0.2 1 1 116 2 0.2 1 0 2 122 1 0.2 1 1 126 1 0.2 1 1 127 1 0.2 1 1 128 1 0.2 1 0 1 130 1 0.2 1 1 131 2 0.2 1 2 132 1 0.2 1 1 133 4 0.2 1 3 1 134 4 0.2 1 4 135 9 0.2 1 8 1 136 57 0.2 1 53 4 137 6015 0.2 1 5914 101 138 16136 0.2 1 15890 246 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041605_val_2.fq.gz ============================================= 13870585 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 685457 (4.9%) 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: 13870585 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 51769 (0.37%)