SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041610_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/processing/cup/BS_workflow/20201110/tmp/c90756ec-5581-11eb-8caf-6c92bfc39744/trimmed/RRBS20A041610_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 219.31 s (23 us/read; 2.65 M reads/minute). === Summary === Total reads processed: 9,676,956 Reads with adapters: 3,806,713 (39.3%) Reads written (passing filters): 9,676,956 (100.0%) Total basepairs processed: 974,662,074 bp Total written (filtered): 946,148,952 bp (97.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3806713 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.8% C: 67.4% G: 6.2% T: 6.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3581501 2419239.0 0 3581501 2 20138 604809.8 0 20138 3 5256 151202.4 0 5256 4 2347 37800.6 0 2347 5 705 9450.2 0 705 6 354 2362.5 0 354 7 685 590.6 0 685 8 397 147.7 0 397 9 206 36.9 0 190 16 10 1528 9.2 1 384 1144 11 57 2.3 1 10 47 12 1202 0.6 1 290 912 13 303 0.1 1 28 275 14 469 0.1 1 50 419 15 158 0.1 1 13 145 16 170 0.1 1 17 153 17 418 0.1 1 46 372 18 169 0.1 1 16 153 19 416 0.1 1 43 373 20 331 0.1 1 31 300 21 41 0.1 1 15 26 22 308 0.1 1 36 272 23 364 0.1 1 30 334 24 1045 0.1 1 90 955 25 346 0.1 1 25 321 26 524 0.1 1 61 463 27 170 0.1 1 17 153 28 360 0.1 1 33 327 29 41 0.1 1 1 40 30 316 0.1 1 35 281 31 252 0.1 1 29 223 32 347 0.1 1 42 305 33 709 0.1 1 80 629 34 252 0.1 1 24 228 35 241 0.1 1 23 218 36 127 0.1 1 14 113 37 310 0.1 1 43 267 38 148 0.1 1 16 132 39 136 0.1 1 20 116 40 128 0.1 1 9 119 41 228 0.1 1 18 210 42 352 0.1 1 36 316 43 149 0.1 1 18 131 44 220 0.1 1 16 204 45 443 0.1 1 53 390 46 206 0.1 1 17 189 47 109 0.1 1 4 105 48 316 0.1 1 32 284 49 183 0.1 1 18 165 50 238 0.1 1 25 213 51 324 0.1 1 33 291 52 275 0.1 1 27 248 53 164 0.1 1 12 152 54 211 0.1 1 20 191 55 193 0.1 1 15 178 56 114 0.1 1 15 99 57 176 0.1 1 16 160 58 266 0.1 1 25 241 59 153 0.1 1 12 141 60 211 0.1 1 26 185 61 270 0.1 1 41 229 62 323 0.1 1 40 283 63 289 0.1 1 52 237 64 121 0.1 1 10 111 65 105 0.1 1 9 96 66 211 0.1 1 17 194 67 157 0.1 1 18 139 68 175 0.1 1 23 152 69 149 0.1 1 19 130 70 161 0.1 1 10 151 71 143 0.1 1 21 122 72 127 0.1 1 12 115 73 130 0.1 1 17 113 74 127 0.1 1 11 116 75 238 0.1 1 20 218 76 241 0.1 1 29 212 77 200 0.1 1 15 185 78 120 0.1 1 13 107 79 137 0.1 1 14 123 80 129 0.1 1 14 115 81 117 0.1 1 11 106 82 132 0.1 1 16 116 83 94 0.1 1 10 84 84 118 0.1 1 17 101 85 124 0.1 1 14 110 86 94 0.1 1 12 82 87 81 0.1 1 8 73 88 61 0.1 1 5 56 89 70 0.1 1 9 61 90 83 0.1 1 10 73 91 63 0.1 1 10 53 92 75 0.1 1 13 62 93 49 0.1 1 7 42 94 81 0.1 1 8 73 95 43 0.1 1 9 34 96 47 0.1 1 3 44 97 42 0.1 1 4 38 98 27 0.1 1 5 22 99 15 0.1 1 5 10 100 36 0.1 1 6 30 101 26 0.1 1 3 23 102 37 0.1 1 5 32 103 18 0.1 1 2 16 104 24 0.1 1 3 21 105 14 0.1 1 3 11 106 10 0.1 1 0 10 107 10 0.1 1 1 9 108 9 0.1 1 1 8 109 8 0.1 1 0 8 110 14 0.1 1 1 13 111 3 0.1 1 2 1 112 2 0.1 1 0 2 116 3 0.1 1 1 2 122 2 0.1 1 1 1 124 2 0.1 1 2 125 1 0.1 1 1 128 2 0.1 1 2 129 5 0.1 1 3 2 130 1 0.1 1 1 131 8 0.1 1 7 1 132 3 0.1 1 2 1 133 6 0.1 1 5 1 134 19 0.1 1 18 1 135 39 0.1 1 35 4 136 161 0.1 1 157 4 137 34404 0.1 1 33824 580 138 139370 0.1 1 137426 1944 139 1 0.1 1 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041610_val_2.fq.gz ============================================= 9676956 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 431927 (4.5%) 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: 9676956 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 201996 (2.09%)