SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041589_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/processing/cup/BS_workflow/20201120/tmp/a5a585f2-5572-11eb-a546-6c92bfc12f0e/trimmed/RRBS20A041589_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 390.10 s (22 us/read; 2.78 M reads/minute). === Summary === Total reads processed: 18,087,775 Reads with adapters: 7,544,684 (41.7%) Reads written (passing filters): 18,087,775 (100.0%) Total basepairs processed: 1,842,405,872 bp Total written (filtered): 1,778,099,289 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7544684 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 0.6% G: 18.4% T: 52.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5254864 4521943.8 0 5254864 2 1459422 1130485.9 0 1459422 3 323830 282621.5 0 323830 4 72840 70655.4 0 72840 5 3350 17663.8 0 3350 6 1323 4416.0 0 1323 7 701 1104.0 0 701 8 457 276.0 0 457 9 798 69.0 0 629 169 10 1302 17.2 1 183 1119 11 1028 4.3 1 100 928 12 447 1.1 1 34 413 13 402 0.3 1 28 374 14 893 0.3 1 69 824 15 499 0.3 1 38 461 16 1620 0.3 1 142 1478 17 1719 0.3 1 172 1547 18 949 0.3 1 201 748 19 48 0.3 1 8 40 20 396 0.3 1 29 367 21 66 0.3 1 10 56 22 94 0.3 1 11 83 23 370 0.3 1 42 328 24 1386 0.3 1 145 1241 25 540 0.3 1 55 485 26 278 0.3 1 23 255 27 475 0.3 1 55 420 28 945 0.3 1 75 870 29 1195 0.3 1 114 1081 30 307 0.3 1 25 282 31 102 0.3 1 3 99 32 499 0.3 1 51 448 33 912 0.3 1 103 809 34 981 0.3 1 99 882 35 569 0.3 1 46 523 36 469 0.3 1 47 422 37 754 0.3 1 83 671 38 196 0.3 1 22 174 39 129 0.3 1 16 113 40 642 0.3 1 55 587 41 348 0.3 1 28 320 42 720 0.3 1 72 648 43 1216 0.3 1 101 1115 44 254 0.3 1 18 236 45 484 0.3 1 58 426 46 191 0.3 1 18 173 47 317 0.3 1 17 300 48 954 0.3 1 93 861 49 129 0.3 1 9 120 50 509 0.3 1 45 464 51 198 0.3 1 13 185 52 113 0.3 1 13 100 53 377 0.3 1 31 346 54 1534 0.3 1 125 1409 55 759 0.3 1 64 695 56 415 0.3 1 37 378 57 647 0.3 1 89 558 58 409 0.3 1 39 370 59 230 0.3 1 28 202 60 360 0.3 1 44 316 61 596 0.3 1 61 535 62 1467 0.3 1 179 1288 63 376 0.3 1 48 328 64 67 0.3 1 3 64 65 60 0.3 1 8 52 66 230 0.3 1 18 212 67 129 0.3 1 8 121 68 480 0.3 1 36 444 69 611 0.3 1 67 544 70 1130 0.3 1 93 1037 71 473 0.3 1 40 433 72 174 0.3 1 16 158 73 226 0.3 1 24 202 74 224 0.3 1 20 204 75 265 0.3 1 20 245 76 310 0.3 1 22 288 77 314 0.3 1 30 284 78 258 0.3 1 20 238 79 284 0.3 1 25 259 80 399 0.3 1 24 375 81 271 0.3 1 19 252 82 264 0.3 1 19 245 83 310 0.3 1 27 283 84 275 0.3 1 25 250 85 326 0.3 1 40 286 86 337 0.3 1 38 299 87 203 0.3 1 19 184 88 171 0.3 1 17 154 89 193 0.3 1 10 183 90 180 0.3 1 13 167 91 154 0.3 1 14 140 92 165 0.3 1 15 150 93 809 0.3 1 58 751 94 968 0.3 1 61 907 95 252 0.3 1 19 233 96 161 0.3 1 14 147 97 1328 0.3 1 74 1254 98 155 0.3 1 15 140 99 116 0.3 1 8 108 100 90 0.3 1 11 79 101 119 0.3 1 6 113 102 277 0.3 1 25 252 103 63 0.3 1 8 55 104 59 0.3 1 3 56 105 41 0.3 1 7 34 106 49 0.3 1 2 47 107 20 0.3 1 1 19 108 12 0.3 1 2 10 109 10 0.3 1 1 9 110 21 0.3 1 3 18 111 5 0.3 1 2 3 112 2 0.3 1 2 113 1 0.3 1 0 1 114 3 0.3 1 1 2 115 2 0.3 1 2 116 2 0.3 1 2 117 4 0.3 1 3 1 119 2 0.3 1 2 120 3 0.3 1 1 2 121 2 0.3 1 2 122 1 0.3 1 1 123 2 0.3 1 2 124 5 0.3 1 1 4 125 3 0.3 1 2 1 126 3 0.3 1 1 2 127 8 0.3 1 8 128 10 0.3 1 9 1 129 5 0.3 1 2 3 130 10 0.3 1 6 4 131 15 0.3 1 9 6 132 24 0.3 1 17 7 133 73 0.3 1 44 29 134 89 0.3 1 73 16 135 131 0.3 1 110 21 136 220 0.3 1 176 44 137 3145 0.3 1 2921 224 138 377479 0.3 1 368917 8562 140 2 0.3 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041589_val_1.fq.gz ============================================= 18087775 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 734182 (4.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 7544684 (41.7%)