SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041586_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/20201104_20201106/tmp/602aec6e-48bc-11eb-9ac6-6c92bfc12d88/trimmed/RRBS20A041586_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 539.07 s (24 us/read; 2.52 M reads/minute). === Summary === Total reads processed: 22,673,732 Reads with adapters: 8,090,192 (35.7%) Reads written (passing filters): 22,673,732 (100.0%) Total basepairs processed: 2,191,531,864 bp Total written (filtered): 2,174,929,236 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8090192 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 15.4% C: 77.6% G: 2.0% T: 5.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7852580 5668433.0 0 7852580 2 87082 1417108.2 0 87082 3 15082 354277.1 0 15082 4 10531 88569.3 0 10531 5 4235 22142.3 0 4235 6 2042 5535.6 0 2042 7 2268 1383.9 0 2268 8 2086 346.0 0 2086 9 1230 86.5 0 1196 34 10 4860 21.6 1 1204 3656 11 562 5.4 1 112 450 12 1019 1.4 1 194 825 13 1189 0.3 1 163 1026 14 1470 0.3 1 199 1271 15 717 0.3 1 73 644 16 1164 0.3 1 161 1003 17 1245 0.3 1 154 1091 18 525 0.3 1 52 473 19 1299 0.3 1 157 1142 20 1448 0.3 1 170 1278 21 92 0.3 1 16 76 22 227 0.3 1 29 198 23 1153 0.3 1 156 997 24 2433 0.3 1 308 2125 25 1123 0.3 1 132 991 26 1822 0.3 1 216 1606 27 1428 0.3 1 190 1238 28 1331 0.3 1 195 1136 29 161 0.3 1 24 137 30 260 0.3 1 36 224 31 271 0.3 1 27 244 32 1159 0.3 1 164 995 33 2517 0.3 1 315 2202 34 699 0.3 1 95 604 35 701 0.3 1 88 613 36 206 0.3 1 17 189 37 1539 0.3 1 213 1326 38 614 0.3 1 57 557 39 741 0.3 1 97 644 40 764 0.3 1 91 673 41 598 0.3 1 73 525 42 873 0.3 1 135 738 43 602 0.3 1 80 522 44 704 0.3 1 78 626 45 1329 0.3 1 193 1136 46 1017 0.3 1 123 894 47 531 0.3 1 56 475 48 994 0.3 1 114 880 49 921 0.3 1 125 796 50 1119 0.3 1 158 961 51 1206 0.3 1 157 1049 52 1107 0.3 1 116 991 53 182 0.3 1 21 161 54 777 0.3 1 76 701 55 1049 0.3 1 134 915 56 181 0.3 1 17 164 57 704 0.3 1 78 626 58 1005 0.3 1 105 900 59 863 0.3 1 101 762 60 1171 0.3 1 176 995 61 1405 0.3 1 193 1212 62 2013 0.3 1 269 1744 63 2191 0.3 1 343 1848 64 1118 0.3 1 142 976 65 708 0.3 1 82 626 66 1449 0.3 1 244 1205 67 742 0.3 1 94 648 68 730 0.3 1 87 643 69 689 0.3 1 84 605 70 676 0.3 1 79 597 71 625 0.3 1 71 554 72 596 0.3 1 58 538 73 572 0.3 1 61 511 74 586 0.3 1 75 511 75 924 0.3 1 150 774 76 790 0.3 1 85 705 77 778 0.3 1 102 676 78 528 0.3 1 55 473 79 546 0.3 1 71 475 80 535 0.3 1 74 461 81 510 0.3 1 53 457 82 556 0.3 1 85 471 83 635 0.3 1 69 566 84 690 0.3 1 83 607 85 937 0.3 1 118 819 86 519 0.3 1 80 439 87 421 0.3 1 54 367 88 427 0.3 1 57 370 89 429 0.3 1 46 383 90 311 0.3 1 40 271 91 294 0.3 1 35 259 92 281 0.3 1 39 242 93 396 0.3 1 41 355 94 403 0.3 1 42 361 95 225 0.3 1 31 194 96 266 0.3 1 40 226 97 285 0.3 1 35 250 98 216 0.3 1 29 187 99 230 0.3 1 32 198 100 212 0.3 1 29 183 101 204 0.3 1 25 179 102 290 0.3 1 25 265 103 119 0.3 1 15 104 104 87 0.3 1 12 75 105 67 0.3 1 6 61 106 61 0.3 1 11 50 107 46 0.3 1 5 41 108 37 0.3 1 5 32 109 53 0.3 1 9 44 110 40 0.3 1 6 34 111 11 0.3 1 1 10 112 3 0.3 1 1 2 113 5 0.3 1 2 3 115 1 0.3 1 1 117 2 0.3 1 1 1 123 3 0.3 1 3 124 1 0.3 1 1 125 2 0.3 1 1 1 127 2 0.3 1 2 128 2 0.3 1 2 129 3 0.3 1 3 130 6 0.3 1 6 131 5 0.3 1 3 2 132 8 0.3 1 6 2 133 5 0.3 1 4 1 134 11 0.3 1 10 1 135 28 0.3 1 23 5 136 73 0.3 1 61 12 137 1358 0.3 1 1283 75 138 32407 0.3 1 31471 936 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041586_val_2.fq.gz ============================================= 22673732 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1510820 (6.7%) 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: 22673732 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 114690 (0.51%)