SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041597_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/a7204e8a-5572-11eb-9350-6c92bfc12e8a/trimmed/RRBS20A041597_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 271.75 s (24 us/read; 2.55 M reads/minute). === Summary === Total reads processed: 11,553,983 Reads with adapters: 4,898,117 (42.4%) Reads written (passing filters): 11,553,983 (100.0%) Total basepairs processed: 1,162,080,577 bp Total written (filtered): 1,130,469,132 bp (97.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4898117 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 18.1% C: 71.0% G: 4.9% T: 6.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4626889 2888495.8 0 4626889 2 43289 722123.9 0 43289 3 6192 180531.0 0 6192 4 3969 45132.7 0 3969 5 1460 11283.2 0 1460 6 630 2820.8 0 630 7 936 705.2 0 936 8 529 176.3 0 529 9 261 44.1 0 236 25 10 2332 11.0 1 584 1748 11 107 2.8 1 17 90 12 1669 0.7 1 367 1302 13 509 0.2 1 34 475 14 593 0.2 1 59 534 15 260 0.2 1 24 236 16 333 0.2 1 25 308 17 617 0.2 1 52 565 18 227 0.2 1 20 207 19 543 0.2 1 52 491 20 447 0.2 1 41 406 21 24 0.2 1 5 19 22 318 0.2 1 42 276 23 488 0.2 1 43 445 24 976 0.2 1 112 864 25 409 0.2 1 32 377 26 690 0.2 1 63 627 27 276 0.2 1 31 245 28 444 0.2 1 42 402 29 57 0.2 1 5 52 30 385 0.2 1 46 339 31 336 0.2 1 47 289 32 394 0.2 1 31 363 33 1011 0.2 1 113 898 34 285 0.2 1 23 262 35 421 0.2 1 41 380 36 102 0.2 1 7 95 37 479 0.2 1 53 426 38 151 0.2 1 15 136 39 216 0.2 1 26 190 40 159 0.2 1 15 144 41 243 0.2 1 20 223 42 349 0.2 1 36 313 43 206 0.2 1 25 181 44 253 0.2 1 23 230 45 546 0.2 1 43 503 46 267 0.2 1 27 240 47 130 0.2 1 13 117 48 320 0.2 1 26 294 49 245 0.2 1 21 224 50 407 0.2 1 48 359 51 446 0.2 1 44 402 52 306 0.2 1 29 277 53 67 0.2 1 7 60 54 227 0.2 1 30 197 55 232 0.2 1 22 210 56 45 0.2 1 5 40 57 169 0.2 1 12 157 58 409 0.2 1 41 368 59 187 0.2 1 18 169 60 282 0.2 1 33 249 61 342 0.2 1 36 306 62 426 0.2 1 75 351 63 361 0.2 1 69 292 64 136 0.2 1 19 117 65 158 0.2 1 24 134 66 352 0.2 1 40 312 67 221 0.2 1 22 199 68 211 0.2 1 21 190 69 177 0.2 1 21 156 70 185 0.2 1 29 156 71 206 0.2 1 16 190 72 196 0.2 1 23 173 73 163 0.2 1 8 155 74 168 0.2 1 14 154 75 295 0.2 1 25 270 76 198 0.2 1 29 169 77 221 0.2 1 18 203 78 134 0.2 1 11 123 79 147 0.2 1 13 134 80 145 0.2 1 14 131 81 135 0.2 1 14 121 82 118 0.2 1 14 104 83 170 0.2 1 18 152 84 211 0.2 1 15 196 85 196 0.2 1 20 176 86 129 0.2 1 17 112 87 117 0.2 1 15 102 88 109 0.2 1 11 98 89 119 0.2 1 13 106 90 87 0.2 1 8 79 91 108 0.2 1 8 100 92 81 0.2 1 9 72 93 118 0.2 1 13 105 94 125 0.2 1 15 110 95 55 0.2 1 9 46 96 77 0.2 1 2 75 97 60 0.2 1 4 56 98 63 0.2 1 8 55 99 57 0.2 1 7 50 100 64 0.2 1 5 59 101 45 0.2 1 2 43 102 54 0.2 1 4 50 103 46 0.2 1 5 41 104 27 0.2 1 4 23 105 24 0.2 1 4 20 106 17 0.2 1 2 15 107 16 0.2 1 3 13 108 13 0.2 1 3 10 109 11 0.2 1 1 10 110 38 0.2 1 3 35 111 3 0.2 1 0 3 112 4 0.2 1 1 3 113 2 0.2 1 1 1 114 1 0.2 1 0 1 115 2 0.2 1 1 1 116 3 0.2 1 2 1 117 1 0.2 1 1 118 2 0.2 1 1 1 120 2 0.2 1 2 122 1 0.2 1 1 125 2 0.2 1 2 126 2 0.2 1 1 1 127 3 0.2 1 3 128 6 0.2 1 6 129 5 0.2 1 5 130 3 0.2 1 3 131 3 0.2 1 3 132 8 0.2 1 8 133 13 0.2 1 12 1 134 15 0.2 1 14 1 135 56 0.2 1 54 2 136 173 0.2 1 163 10 137 15357 0.2 1 15071 286 138 170769 0.2 1 168226 2543 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041597_val_2.fq.gz ============================================= 11553983 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 651849 (5.6%) 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: 11553983 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 228047 (1.97%)