SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041600_val_1.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/c30fca76-3f65-11eb-a036-6c92bfc06fea/trimmed/RRBS20A041600_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 359.43 s (25 us/read; 2.39 M reads/minute). === Summary === Total reads processed: 14,306,385 Reads with adapters: 6,524,427 (45.6%) Reads written (passing filters): 14,306,385 (100.0%) Total basepairs processed: 1,471,927,693 bp Total written (filtered): 1,374,873,877 bp (93.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6524427 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.6% C: 1.2% G: 17.2% T: 43.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4247570 3576596.2 0 4247570 2 1176960 894149.1 0 1176960 3 334955 223537.3 0 334955 4 63369 55884.3 0 63369 5 5680 13971.1 0 5680 6 3503 3492.8 0 3503 7 2423 873.2 0 2423 8 2555 218.3 0 2555 9 2764 54.6 0 2538 226 10 3009 13.6 1 1713 1296 11 1255 3.4 1 127 1128 12 471 0.9 1 36 435 13 565 0.2 1 40 525 14 904 0.2 1 103 801 15 774 0.2 1 70 704 16 1797 0.2 1 249 1548 17 3024 0.2 1 761 2263 18 4050 0.2 1 2821 1229 19 94 0.2 1 21 73 20 541 0.2 1 79 462 21 39 0.2 1 3 36 22 68 0.2 1 6 62 23 493 0.2 1 52 441 24 1281 0.2 1 153 1128 25 600 0.2 1 76 524 26 192 0.2 1 24 168 27 726 0.2 1 96 630 28 1335 0.2 1 191 1144 29 1500 0.2 1 212 1288 30 336 0.2 1 46 290 31 82 0.2 1 9 73 32 635 0.2 1 98 537 33 780 0.2 1 99 681 34 811 0.2 1 94 717 35 1323 0.2 1 166 1157 36 625 0.2 1 76 549 37 342 0.2 1 36 306 38 1230 0.2 1 258 972 39 378 0.2 1 45 333 40 1307 0.2 1 116 1191 41 848 0.2 1 101 747 42 698 0.2 1 57 641 43 1550 0.2 1 166 1384 44 211 0.2 1 15 196 45 774 0.2 1 91 683 46 262 0.2 1 31 231 47 535 0.2 1 54 481 48 1321 0.2 1 132 1189 49 119 0.2 1 9 110 50 656 0.2 1 59 597 51 205 0.2 1 24 181 52 142 0.2 1 11 131 53 415 0.2 1 45 370 54 1097 0.2 1 105 992 55 659 0.2 1 78 581 56 320 0.2 1 28 292 57 626 0.2 1 64 562 58 333 0.2 1 34 299 59 166 0.2 1 12 154 60 377 0.2 1 39 338 61 450 0.2 1 54 396 62 888 0.2 1 100 788 63 320 0.2 1 35 285 64 47 0.2 1 6 41 65 47 0.2 1 4 43 66 154 0.2 1 27 127 67 231 0.2 1 26 205 68 709 0.2 1 81 628 69 731 0.2 1 102 629 70 1206 0.2 1 141 1065 71 609 0.2 1 69 540 72 281 0.2 1 34 247 73 257 0.2 1 40 217 74 272 0.2 1 33 239 75 371 0.2 1 45 326 76 377 0.2 1 51 326 77 343 0.2 1 31 312 78 358 0.2 1 36 322 79 382 0.2 1 59 323 80 324 0.2 1 30 294 81 302 0.2 1 41 261 82 368 0.2 1 40 328 83 293 0.2 1 24 269 84 268 0.2 1 24 244 85 253 0.2 1 27 226 86 381 0.2 1 36 345 87 213 0.2 1 16 197 88 185 0.2 1 11 174 89 176 0.2 1 11 165 90 198 0.2 1 14 184 91 163 0.2 1 11 152 92 162 0.2 1 17 145 93 627 0.2 1 28 599 94 619 0.2 1 25 594 95 241 0.2 1 4 237 96 194 0.2 1 14 180 97 664 0.2 1 18 646 98 118 0.2 1 14 104 99 88 0.2 1 4 84 100 92 0.2 1 8 84 101 107 0.2 1 7 100 102 207 0.2 1 12 195 103 69 0.2 1 7 62 104 50 0.2 1 5 45 105 56 0.2 1 4 52 106 40 0.2 1 6 34 107 36 0.2 1 5 31 108 13 0.2 1 2 11 109 10 0.2 1 2 8 110 45 0.2 1 3 42 111 9 0.2 1 1 8 112 10 0.2 1 2 8 113 8 0.2 1 3 5 114 25 0.2 1 6 19 115 9 0.2 1 4 5 116 19 0.2 1 3 16 117 4 0.2 1 2 2 118 4 0.2 1 2 2 119 1 0.2 1 0 1 121 8 0.2 1 8 122 7 0.2 1 6 1 123 5 0.2 1 3 2 124 4 0.2 1 4 125 6 0.2 1 5 1 126 8 0.2 1 6 2 127 5 0.2 1 4 1 128 19 0.2 1 15 4 129 13 0.2 1 11 2 130 16 0.2 1 13 3 131 34 0.2 1 27 7 132 48 0.2 1 37 11 133 105 0.2 1 76 29 134 157 0.2 1 127 30 135 246 0.2 1 217 29 136 339 0.2 1 306 33 137 5132 0.2 1 4836 296 138 621929 0.2 1 608495 13434 140 2 0.2 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/raw_data/cup/20201121/RRBS20A041600_val_1.fq.gz ============================================= 14306385 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 473890 (3.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 6524420 (45.6%)