SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041594_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/20201104_20201106/tmp/6029eba2-48bc-11eb-ab4d-6c92bfc12b7e/trimmed/RRBS20A041594_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 388.82 s (22 us/read; 2.74 M reads/minute). === Summary === Total reads processed: 17,728,246 Reads with adapters: 6,173,073 (34.8%) Reads written (passing filters): 17,728,246 (100.0%) Total basepairs processed: 1,775,606,814 bp Total written (filtered): 1,753,345,589 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6173073 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.2% C: 68.1% G: 3.1% T: 7.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5944979 4432061.5 0 5944979 2 79753 1108015.4 0 79753 3 5993 277003.8 0 5993 4 3727 69251.0 0 3727 5 1207 17312.7 0 1207 6 688 4328.2 0 688 7 1249 1082.0 0 1249 8 491 270.5 0 491 9 221 67.6 0 193 28 10 2383 16.9 1 486 1897 11 118 4.2 1 15 103 12 1910 1.1 1 341 1569 13 486 0.3 1 68 418 14 525 0.3 1 36 489 15 208 0.3 1 9 199 16 247 0.3 1 19 228 17 436 0.3 1 33 403 18 154 0.3 1 12 142 19 429 0.3 1 26 403 20 309 0.3 1 15 294 21 32 0.3 1 3 29 22 284 0.3 1 23 261 23 424 0.3 1 29 395 24 1033 0.3 1 54 979 25 309 0.3 1 17 292 26 532 0.3 1 35 497 27 181 0.3 1 9 172 28 441 0.3 1 36 405 29 36 0.3 1 0 36 30 351 0.3 1 26 325 31 306 0.3 1 16 290 32 359 0.3 1 18 341 33 782 0.3 1 31 751 34 226 0.3 1 20 206 35 381 0.3 1 30 351 36 48 0.3 1 2 46 37 391 0.3 1 24 367 38 107 0.3 1 12 95 39 129 0.3 1 8 121 40 132 0.3 1 9 123 41 268 0.3 1 18 250 42 447 0.3 1 24 423 43 151 0.3 1 10 141 44 239 0.3 1 13 226 45 563 0.3 1 53 510 46 259 0.3 1 17 242 47 90 0.3 1 7 83 48 414 0.3 1 34 380 49 207 0.3 1 21 186 50 325 0.3 1 18 307 51 399 0.3 1 40 359 52 405 0.3 1 32 373 53 62 0.3 1 2 60 54 243 0.3 1 24 219 55 158 0.3 1 11 147 56 39 0.3 1 2 37 57 159 0.3 1 10 149 58 347 0.3 1 23 324 59 189 0.3 1 14 175 60 252 0.3 1 25 227 61 305 0.3 1 41 264 62 442 0.3 1 70 372 63 394 0.3 1 63 331 64 126 0.3 1 15 111 65 128 0.3 1 9 119 66 335 0.3 1 26 309 67 184 0.3 1 16 168 68 210 0.3 1 15 195 69 175 0.3 1 13 162 70 163 0.3 1 12 151 71 193 0.3 1 19 174 72 183 0.3 1 13 170 73 141 0.3 1 11 130 74 175 0.3 1 13 162 75 338 0.3 1 22 316 76 347 0.3 1 20 327 77 226 0.3 1 10 216 78 183 0.3 1 13 170 79 151 0.3 1 7 144 80 163 0.3 1 14 149 81 133 0.3 1 7 126 82 146 0.3 1 9 137 83 194 0.3 1 10 184 84 202 0.3 1 21 181 85 197 0.3 1 16 181 86 144 0.3 1 10 134 87 92 0.3 1 3 89 88 107 0.3 1 9 98 89 102 0.3 1 7 95 90 80 0.3 1 6 74 91 71 0.3 1 9 62 92 64 0.3 1 4 60 93 84 0.3 1 9 75 94 98 0.3 1 8 90 95 42 0.3 1 4 38 96 65 0.3 1 4 61 97 68 0.3 1 4 64 98 69 0.3 1 2 67 99 75 0.3 1 13 62 100 50 0.3 1 5 45 101 33 0.3 1 3 30 102 64 0.3 1 5 59 103 41 0.3 1 1 40 104 10 0.3 1 0 10 105 11 0.3 1 1 10 106 13 0.3 1 1 12 107 10 0.3 1 0 10 108 17 0.3 1 2 15 109 11 0.3 1 1 10 110 7 0.3 1 1 6 111 4 0.3 1 2 2 112 2 0.3 1 0 2 113 1 0.3 1 1 114 3 0.3 1 3 115 2 0.3 1 1 1 117 2 0.3 1 1 1 118 2 0.3 1 2 120 1 0.3 1 1 121 2 0.3 1 2 122 1 0.3 1 1 124 1 0.3 1 1 125 3 0.3 1 3 126 8 0.3 1 8 127 7 0.3 1 7 128 13 0.3 1 12 1 129 8 0.3 1 7 1 130 8 0.3 1 7 1 131 9 0.3 1 8 1 132 16 0.3 1 15 1 133 26 0.3 1 22 4 134 19 0.3 1 16 3 135 87 0.3 1 81 6 136 262 0.3 1 243 19 137 7236 0.3 1 7036 200 138 101275 0.3 1 99277 1998 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041594_val_2.fq.gz ============================================= 17728246 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 757302 (4.3%) 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: 17728246 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 149093 (0.84%)