SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041596_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/20201120/tmp/a5a96942-5572-11eb-8047-6c92bfc12c02/trimmed/RRBS20A041596_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 277.24 s (23 us/read; 2.58 M reads/minute). === Summary === Total reads processed: 11,900,735 Reads with adapters: 4,286,253 (36.0%) Reads written (passing filters): 11,900,735 (100.0%) Total basepairs processed: 1,201,498,757 bp Total written (filtered): 1,158,383,549 bp (96.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4286253 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 16.3% C: 78.0% G: 0.7% T: 5.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3961761 2975183.8 0 3961761 2 20870 743795.9 0 20870 3 2595 185949.0 0 2595 4 3619 46487.2 0 3619 5 991 11621.8 0 991 6 363 2905.5 0 363 7 672 726.4 0 672 8 535 181.6 0 535 9 204 45.4 0 192 12 10 854 11.3 1 125 729 11 80 2.8 1 8 72 12 178 0.7 1 17 161 13 267 0.2 1 13 254 14 330 0.2 1 24 306 15 159 0.2 1 4 155 16 216 0.2 1 14 202 17 268 0.2 1 15 253 18 129 0.2 1 5 124 19 372 0.2 1 18 354 20 322 0.2 1 26 296 21 17 0.2 1 3 14 22 56 0.2 1 2 54 23 249 0.2 1 12 237 24 670 0.2 1 36 634 25 274 0.2 1 15 259 26 603 0.2 1 34 569 27 127 0.2 1 6 121 28 127 0.2 1 9 118 29 38 0.2 1 3 35 30 63 0.2 1 2 61 31 223 0.2 1 20 203 32 288 0.2 1 21 267 33 846 0.2 1 39 807 34 68 0.2 1 1 67 35 45 0.2 1 3 42 36 49 0.2 1 2 47 37 323 0.2 1 15 308 38 123 0.2 1 8 115 39 165 0.2 1 8 157 40 120 0.2 1 8 112 41 142 0.2 1 5 137 42 283 0.2 1 20 263 43 150 0.2 1 12 138 44 172 0.2 1 13 159 45 413 0.2 1 17 396 46 218 0.2 1 12 206 47 99 0.2 1 3 96 48 269 0.2 1 20 249 49 186 0.2 1 13 173 50 284 0.2 1 12 272 51 336 0.2 1 17 319 52 314 0.2 1 14 300 53 43 0.2 1 3 40 54 171 0.2 1 13 158 55 178 0.2 1 14 164 56 29 0.2 1 1 28 57 116 0.2 1 10 106 58 303 0.2 1 22 281 59 141 0.2 1 14 127 60 209 0.2 1 16 193 61 245 0.2 1 28 217 62 376 0.2 1 85 291 63 373 0.2 1 76 297 64 152 0.2 1 15 137 65 135 0.2 1 16 119 66 417 0.2 1 24 393 67 185 0.2 1 12 173 68 158 0.2 1 11 147 69 123 0.2 1 5 118 70 155 0.2 1 8 147 71 128 0.2 1 14 114 72 130 0.2 1 5 125 73 122 0.2 1 14 108 74 124 0.2 1 11 113 75 209 0.2 1 14 195 76 298 0.2 1 23 275 77 151 0.2 1 7 144 78 116 0.2 1 11 105 79 120 0.2 1 6 114 80 123 0.2 1 10 113 81 125 0.2 1 4 121 82 115 0.2 1 8 107 83 131 0.2 1 5 126 84 197 0.2 1 10 187 85 194 0.2 1 9 185 86 94 0.2 1 4 90 87 62 0.2 1 3 59 88 72 0.2 1 8 64 89 93 0.2 1 7 86 90 65 0.2 1 4 61 91 50 0.2 1 8 42 92 64 0.2 1 1 63 93 67 0.2 1 1 66 94 60 0.2 1 3 57 95 28 0.2 1 2 26 96 45 0.2 1 1 44 97 34 0.2 1 1 33 98 31 0.2 1 1 30 99 37 0.2 1 5 32 100 32 0.2 1 1 31 101 25 0.2 1 2 23 102 31 0.2 1 3 28 103 25 0.2 1 2 23 104 14 0.2 1 2 12 105 5 0.2 1 0 5 106 4 0.2 1 1 3 107 8 0.2 1 0 8 108 8 0.2 1 0 8 109 18 0.2 1 2 16 110 12 0.2 1 1 11 111 1 0.2 1 0 1 113 2 0.2 1 1 1 114 3 0.2 1 2 1 115 3 0.2 1 3 116 3 0.2 1 3 117 2 0.2 1 1 1 118 2 0.2 1 2 119 2 0.2 1 2 121 1 0.2 1 1 122 4 0.2 1 2 2 123 1 0.2 1 1 124 2 0.2 1 2 125 2 0.2 1 2 126 1 0.2 1 1 127 8 0.2 1 8 128 16 0.2 1 14 2 129 15 0.2 1 15 130 13 0.2 1 11 2 131 9 0.2 1 6 3 132 8 0.2 1 8 133 15 0.2 1 14 1 134 29 0.2 1 28 1 135 87 0.2 1 85 2 136 239 0.2 1 226 13 137 3645 0.2 1 3531 114 138 273239 0.2 1 268761 4478 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041596_val_2.fq.gz ============================================= 11900735 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 619333 (5.2%) 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: 11900735 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 303982 (2.55%)