SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041592_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/a5a0f398-5572-11eb-97c5-6c92bfc12b7e/trimmed/RRBS20A041592_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 135.47 s (21 us/read; 2.86 M reads/minute). === Summary === Total reads processed: 6,449,350 Reads with adapters: 2,906,214 (45.1%) Reads written (passing filters): 6,449,350 (100.0%) Total basepairs processed: 686,718,722 bp Total written (filtered): 608,639,254 bp (88.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2906214 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.2% C: 19.4% G: 16.7% T: 39.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1756935 1612337.5 0 1756935 2 455158 403084.4 0 455158 3 108647 100771.1 0 108647 4 25204 25192.8 0 25204 5 1205 6298.2 0 1205 6 671 1574.5 0 671 7 654 393.6 0 654 8 375 98.4 0 375 9 558 24.6 0 479 79 10 695 6.2 1 222 473 11 436 1.5 1 57 379 12 179 0.4 1 19 160 13 185 0.1 1 20 165 14 350 0.1 1 52 298 15 395 0.1 1 64 331 16 1449 0.1 1 575 874 17 1118 0.1 1 174 944 18 386 0.1 1 69 317 19 17 0.1 1 0 17 20 181 0.1 1 23 158 21 34 0.1 1 4 30 22 55 0.1 1 11 44 23 165 0.1 1 28 137 24 620 0.1 1 111 509 25 247 0.1 1 39 208 26 79 0.1 1 11 68 27 223 0.1 1 38 185 28 474 0.1 1 63 411 29 474 0.1 1 87 387 30 140 0.1 1 14 126 31 17 0.1 1 1 16 32 194 0.1 1 31 163 33 380 0.1 1 63 317 34 327 0.1 1 44 283 35 497 0.1 1 79 418 36 243 0.1 1 39 204 37 135 0.1 1 25 110 38 293 0.1 1 37 256 39 150 0.1 1 17 133 40 440 0.1 1 58 382 41 332 0.1 1 42 290 42 362 0.1 1 50 312 43 454 0.1 1 61 393 44 82 0.1 1 8 74 45 186 0.1 1 30 156 46 97 0.1 1 9 88 47 159 0.1 1 19 140 48 508 0.1 1 73 435 49 56 0.1 1 9 47 50 210 0.1 1 27 183 51 86 0.1 1 14 72 52 66 0.1 1 6 60 53 138 0.1 1 14 124 54 420 0.1 1 66 354 55 279 0.1 1 44 235 56 219 0.1 1 34 185 57 184 0.1 1 31 153 58 146 0.1 1 21 125 59 87 0.1 1 7 80 60 86 0.1 1 10 76 61 171 0.1 1 25 146 62 443 0.1 1 59 384 63 107 0.1 1 22 85 64 26 0.1 1 4 22 65 12 0.1 1 2 10 66 60 0.1 1 8 52 67 42 0.1 1 4 38 68 168 0.1 1 19 149 69 203 0.1 1 22 181 70 376 0.1 1 53 323 71 199 0.1 1 25 174 72 70 0.1 1 11 59 73 136 0.1 1 19 117 74 84 0.1 1 18 66 75 104 0.1 1 8 96 76 96 0.1 1 9 87 77 144 0.1 1 24 120 78 99 0.1 1 14 85 79 94 0.1 1 9 85 80 116 0.1 1 14 102 81 83 0.1 1 13 70 82 125 0.1 1 12 113 83 116 0.1 1 19 97 84 91 0.1 1 12 79 85 126 0.1 1 20 106 86 98 0.1 1 17 81 87 76 0.1 1 9 67 88 62 0.1 1 7 55 89 59 0.1 1 7 52 90 68 0.1 1 10 58 91 52 0.1 1 11 41 92 52 0.1 1 4 48 93 129 0.1 1 16 113 94 211 0.1 1 20 191 95 92 0.1 1 8 84 96 59 0.1 1 6 53 97 158 0.1 1 32 126 98 48 0.1 1 8 40 99 35 0.1 1 1 34 100 24 0.1 1 2 22 101 42 0.1 1 7 35 102 65 0.1 1 10 55 103 24 0.1 1 6 18 104 10 0.1 1 1 9 105 18 0.1 1 1 17 106 13 0.1 1 1 12 107 6 0.1 1 1 5 108 8 0.1 1 2 6 109 3 0.1 1 1 2 110 2 0.1 1 0 2 111 2 0.1 1 1 1 112 6 0.1 1 4 2 114 6 0.1 1 2 4 116 1 0.1 1 1 117 3 0.1 1 3 118 1 0.1 1 1 119 3 0.1 1 3 120 1 0.1 1 1 122 2 0.1 1 1 1 123 3 0.1 1 2 1 124 1 0.1 1 1 125 4 0.1 1 3 1 126 2 0.1 1 2 127 9 0.1 1 6 3 128 7 0.1 1 6 1 129 12 0.1 1 9 3 130 10 0.1 1 8 2 131 25 0.1 1 20 5 132 31 0.1 1 25 6 133 78 0.1 1 63 15 134 130 0.1 1 104 26 135 154 0.1 1 130 24 136 260 0.1 1 219 41 137 7175 0.1 1 6855 320 138 529437 0.1 1 517133 12304 140 4 0.1 1 0 4 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041592_val_1.fq.gz ============================================= 6449350 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 240267 (3.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 2906211 (45.1%)