SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041625_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/raw_data/cup/BS_workflow/20201121/tmp/c32f3cb2-3f65-11eb-a561-6c92bfc1302e/trimmed/RRBS20A041625_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 866.59 s (39 us/read; 1.53 M reads/minute). === Summary === Total reads processed: 22,127,674 Reads with adapters: 7,850,945 (35.5%) Reads written (passing filters): 22,127,674 (100.0%) Total basepairs processed: 2,221,092,165 bp Total written (filtered): 1,989,254,662 bp (89.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7850945 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 14.0% C: 80.9% G: 0.6% T: 4.6% 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 6134890 5531918.5 0 6134890 2 47343 1382979.6 0 47343 3 4386 345744.9 0 4386 4 5548 86436.2 0 5548 5 1809 21609.1 0 1809 6 770 5402.3 0 770 7 1153 1350.6 0 1153 8 1035 337.6 0 1035 9 300 84.4 0 278 22 10 1869 21.1 1 374 1495 11 110 5.3 1 9 101 12 278 1.3 1 24 254 13 431 0.3 1 41 390 14 540 0.3 1 35 505 15 257 0.3 1 19 238 16 334 0.3 1 25 309 17 423 0.3 1 26 397 18 220 0.3 1 8 212 19 560 0.3 1 43 517 20 473 0.3 1 49 424 21 39 0.3 1 11 28 22 102 0.3 1 5 97 23 403 0.3 1 24 379 24 995 0.3 1 73 922 25 429 0.3 1 27 402 26 818 0.3 1 37 781 27 224 0.3 1 11 213 28 187 0.3 1 14 173 29 57 0.3 1 2 55 30 106 0.3 1 9 97 31 385 0.3 1 16 369 32 445 0.3 1 24 421 33 1100 0.3 1 56 1044 34 63 0.3 1 1 62 35 82 0.3 1 4 78 36 55 0.3 1 3 52 37 491 0.3 1 33 458 38 175 0.3 1 12 163 39 269 0.3 1 19 250 40 269 0.3 1 14 255 41 312 0.3 1 17 295 42 345 0.3 1 14 331 43 182 0.3 1 10 172 44 280 0.3 1 18 262 45 598 0.3 1 32 566 46 336 0.3 1 11 325 47 185 0.3 1 13 172 48 418 0.3 1 27 391 49 286 0.3 1 19 267 50 403 0.3 1 15 388 51 463 0.3 1 23 440 52 564 0.3 1 33 531 53 63 0.3 1 2 61 54 272 0.3 1 17 255 55 322 0.3 1 22 300 56 53 0.3 1 4 49 57 202 0.3 1 21 181 58 429 0.3 1 24 405 59 234 0.3 1 30 204 60 421 0.3 1 67 354 61 569 0.3 1 152 417 62 968 0.3 1 393 575 63 827 0.3 1 247 580 64 280 0.3 1 52 228 65 213 0.3 1 25 188 66 479 0.3 1 43 436 67 297 0.3 1 28 269 68 266 0.3 1 18 248 69 207 0.3 1 20 187 70 250 0.3 1 31 219 71 195 0.3 1 25 170 72 206 0.3 1 18 188 73 216 0.3 1 20 196 74 232 0.3 1 15 217 75 359 0.3 1 17 342 76 446 0.3 1 37 409 77 316 0.3 1 10 306 78 190 0.3 1 12 178 79 235 0.3 1 16 219 80 244 0.3 1 22 222 81 167 0.3 1 6 161 82 198 0.3 1 8 190 83 257 0.3 1 10 247 84 327 0.3 1 33 294 85 273 0.3 1 20 253 86 181 0.3 1 9 172 87 142 0.3 1 14 128 88 150 0.3 1 15 135 89 104 0.3 1 8 96 90 126 0.3 1 4 122 91 109 0.3 1 5 104 92 118 0.3 1 8 110 93 122 0.3 1 9 113 94 172 0.3 1 18 154 95 84 0.3 1 6 78 96 83 0.3 1 6 77 97 103 0.3 1 5 98 98 93 0.3 1 8 85 99 156 0.3 1 16 140 100 125 0.3 1 4 121 101 122 0.3 1 11 111 102 168 0.3 1 16 152 103 57 0.3 1 2 55 104 40 0.3 1 6 34 105 37 0.3 1 5 32 106 24 0.3 1 0 24 107 18 0.3 1 0 18 108 28 0.3 1 3 25 109 44 0.3 1 7 37 110 30 0.3 1 1 29 111 5 0.3 1 2 3 112 7 0.3 1 2 5 113 19 0.3 1 11 8 114 18 0.3 1 4 14 115 16 0.3 1 14 2 116 11 0.3 1 10 1 117 14 0.3 1 13 1 118 10 0.3 1 10 119 8 0.3 1 5 3 120 9 0.3 1 8 1 121 6 0.3 1 5 1 122 9 0.3 1 9 123 16 0.3 1 9 7 124 17 0.3 1 14 3 125 22 0.3 1 21 1 126 58 0.3 1 53 5 127 85 0.3 1 80 5 128 114 0.3 1 107 7 129 99 0.3 1 95 4 130 100 0.3 1 87 13 131 105 0.3 1 98 7 132 102 0.3 1 85 17 133 182 0.3 1 158 24 134 257 0.3 1 232 25 135 866 0.3 1 796 70 136 2149 0.3 1 2027 122 137 32893 0.3 1 31906 987 138 1587303 0.3 1 1566443 20860 139 1 0.3 1 0 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/raw_data/cup/20201121/RRBS20A041625_val_2.fq.gz ============================================= 22127674 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1034175 (4.7%) 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: 22127674 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1712483 (7.74%)