SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041593_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/20201104_20201106/tmp/5f4d1d8a-48bc-11eb-bbaa-6c92bfc12b72/trimmed/RRBS20A041593_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 223.72 s (22 us/read; 2.70 M reads/minute). === Summary === Total reads processed: 10,050,107 Reads with adapters: 4,097,683 (40.8%) Reads written (passing filters): 10,050,107 (100.0%) Total basepairs processed: 960,864,569 bp Total written (filtered): 948,235,205 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4097683 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 0.6% G: 21.7% T: 47.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2950442 2512526.8 0 2950442 2 827286 628131.7 0 827286 3 184465 157032.9 0 184465 4 43874 39258.2 0 43874 5 3165 9814.6 0 3165 6 1376 2453.6 0 1376 7 786 613.4 0 786 8 783 153.4 0 783 9 1105 38.3 0 985 120 10 1646 9.6 1 580 1066 11 934 2.4 1 123 811 12 475 0.6 1 80 395 13 467 0.1 1 64 403 14 637 0.1 1 62 575 15 641 0.1 1 78 563 16 1536 0.1 1 185 1351 17 2190 0.1 1 364 1826 18 1481 0.1 1 563 918 19 58 0.1 1 7 51 20 493 0.1 1 77 416 21 43 0.1 1 9 34 22 82 0.1 1 10 72 23 581 0.1 1 80 501 24 904 0.1 1 97 807 25 614 0.1 1 88 526 26 139 0.1 1 10 129 27 686 0.1 1 86 600 28 1027 0.1 1 115 912 29 963 0.1 1 139 824 30 391 0.1 1 71 320 31 54 0.1 1 5 49 32 642 0.1 1 104 538 33 1120 0.1 1 141 979 34 1313 0.1 1 184 1129 35 238 0.1 1 28 210 36 790 0.1 1 91 699 37 137 0.1 1 14 123 38 1116 0.1 1 152 964 39 947 0.1 1 127 820 40 335 0.1 1 34 301 41 1061 0.1 1 125 936 42 105 0.1 1 9 96 43 1093 0.1 1 125 968 44 181 0.1 1 19 162 45 775 0.1 1 85 690 46 306 0.1 1 37 269 47 622 0.1 1 59 563 48 1118 0.1 1 101 1017 49 126 0.1 1 6 120 50 678 0.1 1 90 588 51 166 0.1 1 26 140 52 164 0.1 1 16 148 53 534 0.1 1 62 472 54 1091 0.1 1 126 965 55 631 0.1 1 76 555 56 348 0.1 1 34 314 57 677 0.1 1 92 585 58 559 0.1 1 70 489 59 254 0.1 1 24 230 60 524 0.1 1 57 467 61 793 0.1 1 87 706 62 1337 0.1 1 173 1164 63 393 0.1 1 46 347 64 57 0.1 1 6 51 65 80 0.1 1 13 67 66 276 0.1 1 23 253 67 230 0.1 1 25 205 68 643 0.1 1 74 569 69 725 0.1 1 97 628 70 1117 0.1 1 144 973 71 482 0.1 1 60 422 72 308 0.1 1 36 272 73 211 0.1 1 21 190 74 188 0.1 1 25 163 75 247 0.1 1 33 214 76 221 0.1 1 27 194 77 257 0.1 1 24 233 78 278 0.1 1 42 236 79 241 0.1 1 25 216 80 331 0.1 1 35 296 81 299 0.1 1 33 266 82 286 0.1 1 18 268 83 299 0.1 1 30 269 84 277 0.1 1 28 249 85 326 0.1 1 39 287 86 285 0.1 1 26 259 87 194 0.1 1 23 171 88 162 0.1 1 8 154 89 218 0.1 1 18 200 90 178 0.1 1 17 161 91 139 0.1 1 14 125 92 181 0.1 1 14 167 93 433 0.1 1 27 406 94 556 0.1 1 32 524 95 210 0.1 1 13 197 96 148 0.1 1 12 136 97 531 0.1 1 48 483 98 138 0.1 1 17 121 99 76 0.1 1 12 64 100 84 0.1 1 7 77 101 85 0.1 1 4 81 102 168 0.1 1 22 146 103 63 0.1 1 8 55 104 52 0.1 1 4 48 105 42 0.1 1 3 39 106 56 0.1 1 6 50 107 28 0.1 1 6 22 108 11 0.1 1 1 10 109 21 0.1 1 3 18 110 41 0.1 1 3 38 111 3 0.1 1 0 3 112 4 0.1 1 1 3 113 2 0.1 1 1 1 114 5 0.1 1 1 4 115 2 0.1 1 0 2 116 5 0.1 1 0 5 121 1 0.1 1 1 127 1 0.1 1 1 128 3 0.1 1 2 1 129 3 0.1 1 2 1 130 4 0.1 1 1 3 131 1 0.1 1 1 132 7 0.1 1 4 3 133 16 0.1 1 10 6 134 22 0.1 1 19 3 135 17 0.1 1 14 3 136 58 0.1 1 47 11 137 3520 0.1 1 3395 125 138 27657 0.1 1 26749 908 139 36 0.1 1 33 3 140 5339 0.1 1 5200 139 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041593_val_1.fq.gz ============================================= 10050107 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 507362 (5.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 4097682 (40.8%)