SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041627_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/a59f7e8c-5572-11eb-92c8-6c92bfbaf176/trimmed/RRBS20A041627_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 160.83 s (23 us/read; 2.63 M reads/minute). === Summary === Total reads processed: 7,046,374 Reads with adapters: 2,830,284 (40.2%) Reads written (passing filters): 7,046,374 (100.0%) Total basepairs processed: 696,928,309 bp Total written (filtered): 676,843,576 bp (97.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2830284 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.6% C: 69.7% G: 5.5% T: 6.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2657707 1761593.5 0 2657707 2 26629 440398.4 0 26629 3 3969 110099.6 0 3969 4 2505 27524.9 0 2505 5 881 6881.2 0 881 6 322 1720.3 0 322 7 475 430.1 0 475 8 258 107.5 0 258 9 133 26.9 0 119 14 10 1177 6.7 1 274 903 11 51 1.7 1 3 48 12 878 0.4 1 154 724 13 259 0.1 1 20 239 14 349 0.1 1 26 323 15 135 0.1 1 10 125 16 191 0.1 1 20 171 17 319 0.1 1 22 297 18 121 0.1 1 9 112 19 322 0.1 1 24 298 20 249 0.1 1 28 221 21 11 0.1 1 3 8 22 179 0.1 1 14 165 23 260 0.1 1 25 235 24 596 0.1 1 45 551 25 241 0.1 1 26 215 26 380 0.1 1 42 338 27 163 0.1 1 16 147 28 300 0.1 1 29 271 29 22 0.1 1 1 21 30 203 0.1 1 19 184 31 239 0.1 1 29 210 32 258 0.1 1 27 231 33 613 0.1 1 53 560 34 184 0.1 1 17 167 35 255 0.1 1 21 234 36 52 0.1 1 5 47 37 316 0.1 1 34 282 38 102 0.1 1 5 97 39 110 0.1 1 16 94 40 92 0.1 1 6 86 41 150 0.1 1 19 131 42 257 0.1 1 33 224 43 113 0.1 1 17 96 44 167 0.1 1 21 146 45 320 0.1 1 29 291 46 170 0.1 1 12 158 47 85 0.1 1 10 75 48 236 0.1 1 26 210 49 171 0.1 1 15 156 50 320 0.1 1 46 274 51 308 0.1 1 23 285 52 212 0.1 1 17 195 53 43 0.1 1 1 42 54 182 0.1 1 22 160 55 155 0.1 1 11 144 56 34 0.1 1 2 32 57 116 0.1 1 8 108 58 299 0.1 1 28 271 59 141 0.1 1 9 132 60 198 0.1 1 23 175 61 247 0.1 1 34 213 62 298 0.1 1 44 254 63 228 0.1 1 42 186 64 84 0.1 1 10 74 65 104 0.1 1 12 92 66 236 0.1 1 17 219 67 165 0.1 1 21 144 68 166 0.1 1 20 146 69 131 0.1 1 11 120 70 136 0.1 1 17 119 71 115 0.1 1 7 108 72 109 0.1 1 8 101 73 109 0.1 1 8 101 74 115 0.1 1 20 95 75 245 0.1 1 28 217 76 225 0.1 1 11 214 77 167 0.1 1 17 150 78 98 0.1 1 11 87 79 115 0.1 1 13 102 80 110 0.1 1 16 94 81 96 0.1 1 8 88 82 100 0.1 1 15 85 83 99 0.1 1 12 87 84 125 0.1 1 15 110 85 109 0.1 1 10 99 86 78 0.1 1 9 69 87 73 0.1 1 7 66 88 63 0.1 1 3 60 89 86 0.1 1 8 78 90 63 0.1 1 7 56 91 52 0.1 1 8 44 92 46 0.1 1 3 43 93 65 0.1 1 5 60 94 71 0.1 1 5 66 95 34 0.1 1 2 32 96 44 0.1 1 4 40 97 43 0.1 1 2 41 98 32 0.1 1 2 30 99 41 0.1 1 5 36 100 29 0.1 1 2 27 101 24 0.1 1 3 21 102 40 0.1 1 2 38 103 22 0.1 1 6 16 104 16 0.1 1 2 14 105 12 0.1 1 2 10 106 6 0.1 1 0 6 107 3 0.1 1 1 2 108 7 0.1 1 0 7 109 6 0.1 1 0 6 110 30 0.1 1 2 28 111 1 0.1 1 0 1 112 1 0.1 1 0 1 114 2 0.1 1 0 2 116 4 0.1 1 0 4 117 1 0.1 1 1 120 1 0.1 1 1 123 1 0.1 1 1 124 1 0.1 1 1 126 2 0.1 1 2 127 4 0.1 1 4 128 2 0.1 1 1 1 129 2 0.1 1 2 130 2 0.1 1 2 131 3 0.1 1 3 132 2 0.1 1 2 133 5 0.1 1 5 134 8 0.1 1 5 3 135 21 0.1 1 17 4 136 104 0.1 1 101 3 137 8476 0.1 1 8321 155 138 111739 0.1 1 110265 1474 139 1 0.1 1 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041627_val_2.fq.gz ============================================= 7046374 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 388060 (5.5%) 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: 7046374 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 145153 (2.06%)