SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000234_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/f9776294-1990-11ec-b146-6c92bfc12eb4/trimmed/RRBS21T000234_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 919.60 s (25 us/read; 2.37 M reads/minute). === Summary === Total reads processed: 36,279,302 Reads with adapters: 24,153,102 (66.6%) Reads written (passing filters): 36,279,302 (100.0%) Total basepairs processed: 3,422,589,317 bp Total written (filtered): 2,321,606,591 bp (67.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24153102 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 3.2% C: 95.9% G: 0.1% T: 0.8% none/other: 0.0% WARNING: The adapter is preceded by "C" 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 16232900 9069825.5 0 16232900 2 19059 2267456.4 0 19059 3 7470 566864.1 0 7470 4 6107 141716.0 0 6107 5 1197 35429.0 0 1197 6 687 8857.3 0 687 7 896 2214.3 0 896 8 822 553.6 0 822 9 652 138.4 0 627 25 10 3304 34.6 1 769 2535 11 236 8.6 1 47 189 12 498 2.2 1 85 413 13 672 0.5 1 56 616 14 745 0.5 1 68 677 15 310 0.5 1 28 282 16 722 0.5 1 66 656 17 953 0.5 1 71 882 18 285 0.5 1 29 256 19 867 0.5 1 56 811 20 625 0.5 1 75 550 21 406 0.5 1 255 151 22 220 0.5 1 21 199 23 510 0.5 1 29 481 24 1341 0.5 1 87 1254 25 531 0.5 1 42 489 26 530 0.5 1 52 478 27 324 0.5 1 48 276 28 363 0.5 1 45 318 29 127 0.5 1 8 119 30 333 0.5 1 24 309 31 229 0.5 1 17 212 32 543 0.5 1 46 497 33 487 0.5 1 44 443 34 263 0.5 1 17 246 35 420 0.5 1 28 392 36 321 0.5 1 21 300 37 296 0.5 1 23 273 38 264 0.5 1 20 244 39 286 0.5 1 23 263 40 231 0.5 1 14 217 41 427 0.5 1 15 412 42 404 0.5 1 26 378 43 238 0.5 1 18 220 44 317 0.5 1 21 296 45 435 0.5 1 38 397 46 313 0.5 1 19 294 47 271 0.5 1 16 255 48 575 0.5 1 43 532 49 424 0.5 1 31 393 50 238 0.5 1 13 225 51 462 0.5 1 32 430 52 566 0.5 1 34 532 53 383 0.5 1 21 362 54 394 0.5 1 20 374 55 359 0.5 1 26 333 56 272 0.5 1 15 257 57 374 0.5 1 18 356 58 250 0.5 1 18 232 59 249 0.5 1 17 232 60 233 0.5 1 12 221 61 181 0.5 1 16 165 62 192 0.5 1 17 175 63 211 0.5 1 21 190 64 205 0.5 1 22 183 65 262 0.5 1 21 241 66 518 0.5 1 47 471 67 306 0.5 1 23 283 68 339 0.5 1 29 310 69 304 0.5 1 18 286 70 329 0.5 1 34 295 71 333 0.5 1 25 308 72 339 0.5 1 31 308 73 308 0.5 1 27 281 74 262 0.5 1 36 226 75 457 0.5 1 40 417 76 561 0.5 1 42 519 77 338 0.5 1 27 311 78 222 0.5 1 11 211 79 251 0.5 1 16 235 80 169 0.5 1 4 165 81 166 0.5 1 14 152 82 147 0.5 1 11 136 83 151 0.5 1 11 140 84 115 0.5 1 6 109 85 117 0.5 1 11 106 86 111 0.5 1 7 104 87 86 0.5 1 8 78 88 88 0.5 1 4 84 89 80 0.5 1 11 69 90 84 0.5 1 7 77 91 122 0.5 1 8 114 92 77 0.5 1 1 76 93 110 0.5 1 9 101 94 110 0.5 1 9 101 95 79 0.5 1 10 69 96 157 0.5 1 11 146 97 68 0.5 1 10 58 98 92 0.5 1 4 88 99 107 0.5 1 8 99 100 79 0.5 1 9 70 101 47 0.5 1 4 43 102 81 0.5 1 9 72 103 28 0.5 1 3 25 104 56 0.5 1 5 51 105 28 0.5 1 4 24 106 33 0.5 1 1 32 107 20 0.5 1 1 19 108 19 0.5 1 6 13 109 16 0.5 1 0 16 110 17 0.5 1 5 12 111 9 0.5 1 3 6 112 8 0.5 1 1 7 113 7 0.5 1 4 3 114 18 0.5 1 8 10 115 7 0.5 1 6 1 116 9 0.5 1 8 1 117 6 0.5 1 5 1 118 6 0.5 1 3 3 119 3 0.5 1 2 1 120 10 0.5 1 6 4 121 6 0.5 1 6 122 5 0.5 1 5 123 4 0.5 1 4 124 15 0.5 1 13 2 125 16 0.5 1 14 2 126 12 0.5 1 12 127 37 0.5 1 33 4 128 54 0.5 1 53 1 129 76 0.5 1 74 2 130 68 0.5 1 61 7 131 90 0.5 1 84 6 132 118 0.5 1 111 7 133 145 0.5 1 129 16 134 239 0.5 1 224 15 135 957 0.5 1 891 66 136 2170 0.5 1 2071 99 137 72510 0.5 1 70781 1729 138 7773695 0.5 1 7667906 105789 139 8 0.5 1 7 1 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_20210722/clean_data/RRBS21T000234_val_2.fq.gz ============================================= 36279302 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 949132 (2.6%) 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: 36279302 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 7928170 (21.85%)