SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041596_val_1.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_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 266.27 s (22 us/read; 2.68 M reads/minute). === Summary === Total reads processed: 11,900,735 Reads with adapters: 5,009,013 (42.1%) Reads written (passing filters): 11,900,735 (100.0%) Total basepairs processed: 1,211,723,378 bp Total written (filtered): 1,165,461,851 bp (96.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5009013 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 6.6% G: 19.8% T: 43.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3495376 2975183.8 0 3495376 2 912135 743795.9 0 912135 3 226521 185949.0 0 226521 4 52793 46487.2 0 52793 5 2370 11621.8 0 2370 6 1291 2905.5 0 1291 7 1354 726.4 0 1354 8 676 181.6 0 676 9 1095 45.4 0 926 169 10 1219 11.3 1 403 816 11 844 2.8 1 97 747 12 349 0.7 1 41 308 13 314 0.2 1 30 284 14 689 0.2 1 72 617 15 532 0.2 1 74 458 16 1550 0.2 1 303 1247 17 1455 0.2 1 203 1252 18 589 0.2 1 96 493 19 36 0.2 1 4 32 20 296 0.2 1 56 240 21 66 0.2 1 6 60 22 83 0.2 1 16 67 23 342 0.2 1 39 303 24 1242 0.2 1 236 1006 25 433 0.2 1 63 370 26 187 0.2 1 23 164 27 450 0.2 1 50 400 28 1018 0.2 1 121 897 29 1008 0.2 1 158 850 30 261 0.2 1 52 209 31 31 0.2 1 4 27 32 336 0.2 1 48 288 33 830 0.2 1 107 723 34 723 0.2 1 96 627 35 1164 0.2 1 171 993 36 531 0.2 1 70 461 37 244 0.2 1 34 210 38 700 0.2 1 94 606 39 361 0.2 1 53 308 40 888 0.2 1 99 789 41 667 0.2 1 74 593 42 756 0.2 1 110 646 43 948 0.2 1 110 838 44 201 0.2 1 18 183 45 502 0.2 1 74 428 46 191 0.2 1 18 173 47 286 0.2 1 27 259 48 1062 0.2 1 145 917 49 139 0.2 1 16 123 50 391 0.2 1 57 334 51 183 0.2 1 29 154 52 146 0.2 1 20 126 53 307 0.2 1 49 258 54 972 0.2 1 127 845 55 634 0.2 1 81 553 56 528 0.2 1 70 458 57 393 0.2 1 49 344 58 261 0.2 1 26 235 59 163 0.2 1 29 134 60 224 0.2 1 33 191 61 410 0.2 1 44 366 62 1029 0.2 1 135 894 63 246 0.2 1 23 223 64 55 0.2 1 10 45 65 33 0.2 1 6 27 66 135 0.2 1 10 125 67 117 0.2 1 15 102 68 407 0.2 1 49 358 69 437 0.2 1 54 383 70 785 0.2 1 102 683 71 415 0.2 1 46 369 72 134 0.2 1 14 120 73 249 0.2 1 39 210 74 218 0.2 1 36 182 75 216 0.2 1 21 195 76 193 0.2 1 26 167 77 258 0.2 1 37 221 78 212 0.2 1 17 195 79 231 0.2 1 32 199 80 207 0.2 1 20 187 81 190 0.2 1 21 169 82 228 0.2 1 35 193 83 271 0.2 1 50 221 84 198 0.2 1 30 168 85 292 0.2 1 39 253 86 199 0.2 1 24 175 87 128 0.2 1 16 112 88 150 0.2 1 20 130 89 157 0.2 1 23 134 90 148 0.2 1 18 130 91 137 0.2 1 18 119 92 140 0.2 1 27 113 93 260 0.2 1 36 224 94 293 0.2 1 37 256 95 107 0.2 1 12 95 96 102 0.2 1 8 94 97 188 0.2 1 21 167 98 70 0.2 1 10 60 99 55 0.2 1 4 51 100 49 0.2 1 6 43 101 75 0.2 1 15 60 102 76 0.2 1 14 62 103 42 0.2 1 7 35 104 17 0.2 1 2 15 105 23 0.2 1 4 19 106 21 0.2 1 1 20 107 15 0.2 1 4 11 108 9 0.2 1 2 7 109 8 0.2 1 2 6 110 10 0.2 1 4 6 111 3 0.2 1 2 1 112 4 0.2 1 2 2 114 1 0.2 1 0 1 115 3 0.2 1 2 1 116 2 0.2 1 0 2 117 1 0.2 1 0 1 119 1 0.2 1 1 120 2 0.2 1 0 2 121 2 0.2 1 2 122 1 0.2 1 1 123 2 0.2 1 2 124 4 0.2 1 4 125 1 0.2 1 0 1 126 4 0.2 1 4 127 10 0.2 1 3 7 128 5 0.2 1 2 3 129 9 0.2 1 6 3 130 6 0.2 1 5 1 131 6 0.2 1 5 1 132 8 0.2 1 5 3 133 34 0.2 1 25 9 134 66 0.2 1 52 14 135 84 0.2 1 70 14 136 129 0.2 1 110 19 137 3299 0.2 1 3135 164 138 274340 0.2 1 265912 8428 140 5 0.2 1 0 5 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041596_val_1.fq.gz ============================================= 11900735 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 430936 (3.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 5009011 (42.1%)