SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041522_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/20201110/tmp/cbb16130-5581-11eb-b8bb-6c92bfc1303a/trimmed/RRBS20A041522_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 281.10 s (23 us/read; 2.62 M reads/minute). === Summary === Total reads processed: 12,262,650 Reads with adapters: 5,050,732 (41.2%) Reads written (passing filters): 12,262,650 (100.0%) Total basepairs processed: 1,174,051,933 bp Total written (filtered): 1,148,418,825 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5050732 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 17.7% C: 72.5% G: 3.9% T: 5.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4849077 3065662.5 0 4849077 2 24774 766415.6 0 24774 3 3312 191603.9 0 3312 4 2331 47901.0 0 2331 5 892 11975.2 0 892 6 470 2993.8 0 470 7 894 748.5 0 894 8 499 187.1 0 499 9 278 46.8 0 258 20 10 1466 11.7 1 395 1071 11 70 2.9 1 10 60 12 1240 0.7 1 312 928 13 346 0.2 1 40 306 14 517 0.2 1 68 449 15 226 0.2 1 35 191 16 214 0.2 1 17 197 17 495 0.2 1 61 434 18 161 0.2 1 15 146 19 530 0.2 1 54 476 20 378 0.2 1 43 335 21 24 0.2 1 7 17 22 292 0.2 1 30 262 23 398 0.2 1 46 352 24 1230 0.2 1 153 1077 25 304 0.2 1 22 282 26 636 0.2 1 74 562 27 204 0.2 1 30 174 28 313 0.2 1 26 287 29 40 0.2 1 3 37 30 301 0.2 1 27 274 31 336 0.2 1 51 285 32 384 0.2 1 56 328 33 1076 0.2 1 147 929 34 321 0.2 1 39 282 35 274 0.2 1 34 240 36 74 0.2 1 6 68 37 452 0.2 1 55 397 38 128 0.2 1 14 114 39 148 0.2 1 24 124 40 145 0.2 1 16 129 41 214 0.2 1 24 190 42 412 0.2 1 49 363 43 157 0.2 1 18 139 44 255 0.2 1 18 237 45 645 0.2 1 81 564 46 284 0.2 1 30 254 47 72 0.2 1 9 63 48 383 0.2 1 45 338 49 184 0.2 1 19 165 50 411 0.2 1 51 360 51 446 0.2 1 51 395 52 315 0.2 1 33 282 53 48 0.2 1 4 44 54 233 0.2 1 22 211 55 165 0.2 1 21 144 56 28 0.2 1 1 27 57 163 0.2 1 15 148 58 467 0.2 1 51 416 59 234 0.2 1 21 213 60 399 0.2 1 49 350 61 468 0.2 1 64 404 62 559 0.2 1 82 477 63 475 0.2 1 81 394 64 134 0.2 1 25 109 65 112 0.2 1 10 102 66 231 0.2 1 21 210 67 265 0.2 1 34 231 68 284 0.2 1 40 244 69 249 0.2 1 30 219 70 242 0.2 1 23 219 71 222 0.2 1 28 194 72 235 0.2 1 19 216 73 192 0.2 1 20 172 74 223 0.2 1 23 200 75 379 0.2 1 44 335 76 244 0.2 1 26 218 77 309 0.2 1 32 277 78 202 0.2 1 24 178 79 221 0.2 1 25 196 80 197 0.2 1 22 175 81 190 0.2 1 21 169 82 211 0.2 1 23 188 83 211 0.2 1 20 191 84 292 0.2 1 28 264 85 226 0.2 1 18 208 86 197 0.2 1 25 172 87 173 0.2 1 19 154 88 146 0.2 1 14 132 89 168 0.2 1 22 146 90 153 0.2 1 13 140 91 127 0.2 1 17 110 92 138 0.2 1 21 117 93 144 0.2 1 15 129 94 172 0.2 1 22 150 95 70 0.2 1 9 61 96 86 0.2 1 11 75 97 90 0.2 1 10 80 98 69 0.2 1 10 59 99 83 0.2 1 6 77 100 77 0.2 1 8 69 101 59 0.2 1 8 51 102 68 0.2 1 14 54 103 57 0.2 1 8 49 104 29 0.2 1 2 27 105 32 0.2 1 5 27 106 10 0.2 1 1 9 107 18 0.2 1 2 16 108 12 0.2 1 1 11 109 18 0.2 1 1 17 110 42 0.2 1 11 31 111 6 0.2 1 4 2 112 1 0.2 1 0 1 114 2 0.2 1 0 2 115 1 0.2 1 0 1 116 2 0.2 1 1 1 120 1 0.2 1 0 1 122 1 0.2 1 0 1 124 1 0.2 1 1 125 1 0.2 1 1 126 4 0.2 1 4 127 4 0.2 1 4 128 2 0.2 1 2 129 3 0.2 1 3 130 4 0.2 1 3 1 131 6 0.2 1 5 1 132 6 0.2 1 6 133 10 0.2 1 8 2 134 11 0.2 1 10 1 135 26 0.2 1 24 2 136 174 0.2 1 156 18 137 28236 0.2 1 27824 412 138 112653 0.2 1 111190 1463 139 1 0.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041522_val_2.fq.gz ============================================= 12262650 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 587409 (4.8%) 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: 12262650 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 186387 (1.52%)