SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041604_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/a5a39dd2-5572-11eb-a07c-6c92bfc12ecc/trimmed/RRBS20A041604_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 276.91 s (22 us/read; 2.75 M reads/minute). === Summary === Total reads processed: 12,691,001 Reads with adapters: 5,641,482 (44.5%) Reads written (passing filters): 12,691,001 (100.0%) Total basepairs processed: 1,334,601,561 bp Total written (filtered): 1,272,343,811 bp (95.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5641482 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 0.7% G: 18.3% T: 44.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3854485 3172750.2 0 3854485 2 1033890 793187.6 0 1033890 3 265716 198296.9 0 265716 4 55640 49574.2 0 55640 5 2945 12393.6 0 2945 6 1665 3098.4 0 1665 7 1348 774.6 0 1348 8 778 193.6 0 778 9 1049 48.4 0 910 139 10 1416 12.1 1 504 912 11 831 3.0 1 69 762 12 294 0.8 1 30 264 13 325 0.2 1 36 289 14 644 0.2 1 54 590 15 368 0.2 1 46 322 16 1439 0.2 1 176 1263 17 1659 0.2 1 317 1342 18 1953 0.2 1 1282 671 19 52 0.2 1 8 44 20 282 0.2 1 39 243 21 52 0.2 1 3 49 22 77 0.2 1 7 70 23 287 0.2 1 26 261 24 1154 0.2 1 140 1014 25 396 0.2 1 36 360 26 193 0.2 1 14 179 27 396 0.2 1 41 355 28 805 0.2 1 102 703 29 906 0.2 1 103 803 30 235 0.2 1 38 197 31 88 0.2 1 10 78 32 405 0.2 1 53 352 33 723 0.2 1 74 649 34 680 0.2 1 81 599 35 475 0.2 1 60 415 36 389 0.2 1 55 334 37 691 0.2 1 82 609 38 461 0.2 1 191 270 39 81 0.2 1 11 70 40 504 0.2 1 36 468 41 379 0.2 1 46 333 42 497 0.2 1 50 447 43 840 0.2 1 70 770 44 183 0.2 1 13 170 45 386 0.2 1 37 349 46 126 0.2 1 15 111 47 237 0.2 1 13 224 48 708 0.2 1 62 646 49 49 0.2 1 2 47 50 411 0.2 1 50 361 51 122 0.2 1 14 108 52 92 0.2 1 5 87 53 277 0.2 1 18 259 54 811 0.2 1 66 745 55 486 0.2 1 39 447 56 375 0.2 1 37 338 57 335 0.2 1 35 300 58 267 0.2 1 26 241 59 151 0.2 1 17 134 60 211 0.2 1 14 197 61 375 0.2 1 46 329 62 824 0.2 1 108 716 63 220 0.2 1 18 202 64 37 0.2 1 3 34 65 28 0.2 1 2 26 66 104 0.2 1 8 96 67 101 0.2 1 10 91 68 350 0.2 1 39 311 69 444 0.2 1 65 379 70 897 0.2 1 81 816 71 438 0.2 1 31 407 72 161 0.2 1 13 148 73 204 0.2 1 26 178 74 213 0.2 1 26 187 75 222 0.2 1 31 191 76 182 0.2 1 19 163 77 194 0.2 1 23 171 78 197 0.2 1 13 184 79 177 0.2 1 17 160 80 179 0.2 1 17 162 81 185 0.2 1 12 173 82 196 0.2 1 13 183 83 199 0.2 1 29 170 84 162 0.2 1 12 150 85 229 0.2 1 26 203 86 158 0.2 1 8 150 87 116 0.2 1 11 105 88 107 0.2 1 9 98 89 105 0.2 1 9 96 90 120 0.2 1 11 109 91 83 0.2 1 3 80 92 97 0.2 1 17 80 93 174 0.2 1 17 157 94 238 0.2 1 9 229 95 88 0.2 1 8 80 96 97 0.2 1 7 90 97 160 0.2 1 13 147 98 66 0.2 1 4 62 99 41 0.2 1 1 40 100 41 0.2 1 4 37 101 45 0.2 1 6 39 102 86 0.2 1 6 80 103 33 0.2 1 5 28 104 13 0.2 1 4 9 105 25 0.2 1 5 20 106 17 0.2 1 3 14 107 16 0.2 1 4 12 108 5 0.2 1 1 4 109 7 0.2 1 2 5 110 4 0.2 1 0 4 111 5 0.2 1 0 5 112 2 0.2 1 1 1 113 3 0.2 1 2 1 114 16 0.2 1 2 14 115 2 0.2 1 1 1 116 14 0.2 1 3 11 117 3 0.2 1 2 1 119 1 0.2 1 0 1 121 1 0.2 1 0 1 123 4 0.2 1 3 1 124 6 0.2 1 6 125 4 0.2 1 2 2 126 4 0.2 1 4 127 9 0.2 1 8 1 128 4 0.2 1 3 1 129 10 0.2 1 9 1 130 5 0.2 1 4 1 131 13 0.2 1 10 3 132 24 0.2 1 19 5 133 36 0.2 1 28 8 134 97 0.2 1 83 14 135 128 0.2 1 107 21 136 169 0.2 1 150 19 137 2623 0.2 1 2476 147 138 387111 0.2 1 379777 7334 139 2 0.2 1 0 2 140 6 0.2 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041604_val_1.fq.gz ============================================= 12691001 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 398546 (3.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 5641479 (44.5%)