SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041584_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/c9157a74-5581-11eb-8d91-6c92bfc39756/trimmed/RRBS20A041584_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 457.23 s (26 us/read; 2.28 M reads/minute). === Summary === Total reads processed: 17,379,964 Reads with adapters: 7,006,660 (40.3%) Reads written (passing filters): 17,379,964 (100.0%) Total basepairs processed: 1,677,604,511 bp Total written (filtered): 1,640,038,748 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7006660 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 13.9% C: 77.8% G: 0.6% T: 7.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6733758 4344991.0 0 6733758 2 19766 1086247.8 0 19766 3 4910 271561.9 0 4910 4 5118 67890.5 0 5118 5 1176 16972.6 0 1176 6 590 4243.2 0 590 7 1037 1060.8 0 1037 8 640 265.2 0 640 9 431 66.3 0 422 9 10 1484 16.6 1 311 1173 11 160 4.1 1 32 128 12 306 1.0 1 25 281 13 419 0.3 1 55 364 14 517 0.3 1 50 467 15 218 0.3 1 18 200 16 297 0.3 1 35 262 17 446 0.3 1 55 391 18 189 0.3 1 13 176 19 526 0.3 1 54 472 20 365 0.3 1 32 333 21 16 0.3 1 5 11 22 98 0.3 1 10 88 23 436 0.3 1 41 395 24 1294 0.3 1 140 1154 25 340 0.3 1 28 312 26 671 0.3 1 66 605 27 451 0.3 1 56 395 28 293 0.3 1 32 261 29 50 0.3 1 5 45 30 99 0.3 1 16 83 31 81 0.3 1 5 76 32 484 0.3 1 46 438 33 1013 0.3 1 101 912 34 257 0.3 1 36 221 35 199 0.3 1 19 180 36 61 0.3 1 7 54 37 442 0.3 1 36 406 38 128 0.3 1 9 119 39 154 0.3 1 15 139 40 163 0.3 1 16 147 41 170 0.3 1 16 154 42 411 0.3 1 52 359 43 196 0.3 1 17 179 44 268 0.3 1 18 250 45 643 0.3 1 54 589 46 309 0.3 1 29 280 47 89 0.3 1 7 82 48 384 0.3 1 30 354 49 193 0.3 1 22 171 50 308 0.3 1 25 283 51 376 0.3 1 26 350 52 422 0.3 1 45 377 53 44 0.3 1 4 40 54 198 0.3 1 10 188 55 209 0.3 1 15 194 56 43 0.3 1 9 34 57 154 0.3 1 13 141 58 303 0.3 1 33 270 59 179 0.3 1 14 165 60 300 0.3 1 29 271 61 451 0.3 1 65 386 62 490 0.3 1 69 421 63 429 0.3 1 59 370 64 166 0.3 1 16 150 65 120 0.3 1 6 114 66 275 0.3 1 31 244 67 214 0.3 1 28 186 68 238 0.3 1 23 215 69 194 0.3 1 24 170 70 191 0.3 1 19 172 71 181 0.3 1 12 169 72 208 0.3 1 13 195 73 202 0.3 1 21 181 74 209 0.3 1 18 191 75 307 0.3 1 33 274 76 352 0.3 1 44 308 77 231 0.3 1 15 216 78 171 0.3 1 11 160 79 160 0.3 1 13 147 80 166 0.3 1 23 143 81 179 0.3 1 10 169 82 220 0.3 1 28 192 83 249 0.3 1 17 232 84 225 0.3 1 18 207 85 209 0.3 1 18 191 86 161 0.3 1 12 149 87 121 0.3 1 13 108 88 128 0.3 1 15 113 89 120 0.3 1 10 110 90 113 0.3 1 13 100 91 90 0.3 1 5 85 92 109 0.3 1 12 97 93 110 0.3 1 5 105 94 109 0.3 1 5 104 95 57 0.3 1 8 49 96 58 0.3 1 2 56 97 77 0.3 1 5 72 98 69 0.3 1 5 64 99 85 0.3 1 9 76 100 59 0.3 1 10 49 101 46 0.3 1 2 44 102 60 0.3 1 7 53 103 34 0.3 1 1 33 104 30 0.3 1 5 25 105 25 0.3 1 1 24 106 11 0.3 1 0 11 107 9 0.3 1 2 7 108 11 0.3 1 0 11 109 18 0.3 1 1 17 110 21 0.3 1 0 21 111 9 0.3 1 1 8 116 2 0.3 1 1 1 120 1 0.3 1 1 122 1 0.3 1 1 123 1 0.3 1 0 1 124 1 0.3 1 1 125 3 0.3 1 2 1 126 4 0.3 1 3 1 127 2 0.3 1 2 128 10 0.3 1 8 2 129 3 0.3 1 3 130 5 0.3 1 4 1 131 10 0.3 1 9 1 132 8 0.3 1 7 1 133 15 0.3 1 13 2 134 15 0.3 1 13 2 135 46 0.3 1 41 5 136 96 0.3 1 82 14 137 3876 0.3 1 3770 106 138 210502 0.3 1 206792 3710 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041584_val_2.fq.gz ============================================= 17379964 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 812562 (4.7%) 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: 17379964 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 272354 (1.57%)