SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041630_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/602907e6-48bc-11eb-ac9d-6c92bfc12b7e/trimmed/RRBS20A041630_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 434.15 s (24 us/read; 2.51 M reads/minute). === Summary === Total reads processed: 18,184,059 Reads with adapters: 6,979,941 (38.4%) Reads written (passing filters): 18,184,059 (100.0%) Total basepairs processed: 1,784,214,656 bp Total written (filtered): 1,765,950,113 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6979941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.4% C: 64.9% G: 3.3% T: 8.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6695118 4546014.8 0 6695118 2 103546 1136503.7 0 103546 3 12586 284125.9 0 12586 4 10119 71031.5 0 10119 5 4121 17757.9 0 4121 6 2366 4439.5 0 2366 7 2939 1109.9 0 2939 8 1709 277.5 0 1709 9 862 69.4 0 808 54 10 6325 17.3 1 2171 4154 11 308 4.3 1 59 249 12 4568 1.1 1 1434 3134 13 1390 0.3 1 296 1094 14 2126 0.3 1 365 1761 15 925 0.3 1 156 769 16 985 0.3 1 171 814 17 1703 0.3 1 311 1392 18 887 0.3 1 138 749 19 1766 0.3 1 338 1428 20 1632 0.3 1 307 1325 21 106 0.3 1 18 88 22 1246 0.3 1 221 1025 23 1558 0.3 1 310 1248 24 2978 0.3 1 534 2444 25 1317 0.3 1 216 1101 26 1724 0.3 1 320 1404 27 878 0.3 1 155 723 28 1802 0.3 1 367 1435 29 154 0.3 1 28 126 30 1358 0.3 1 243 1115 31 1396 0.3 1 239 1157 32 1449 0.3 1 289 1160 33 3075 0.3 1 603 2472 34 979 0.3 1 199 780 35 1773 0.3 1 349 1424 36 355 0.3 1 52 303 37 1890 0.3 1 369 1521 38 683 0.3 1 147 536 39 791 0.3 1 139 652 40 679 0.3 1 126 553 41 780 0.3 1 130 650 42 1035 0.3 1 212 823 43 698 0.3 1 114 584 44 829 0.3 1 133 696 45 1410 0.3 1 235 1175 46 940 0.3 1 151 789 47 590 0.3 1 91 499 48 1238 0.3 1 203 1035 49 902 0.3 1 153 749 50 1147 0.3 1 239 908 51 1416 0.3 1 270 1146 52 1161 0.3 1 163 998 53 240 0.3 1 35 205 54 965 0.3 1 148 817 55 995 0.3 1 165 830 56 161 0.3 1 30 131 57 792 0.3 1 122 670 58 1369 0.3 1 205 1164 59 912 0.3 1 170 742 60 1271 0.3 1 243 1028 61 1519 0.3 1 286 1233 62 2031 0.3 1 369 1662 63 2074 0.3 1 407 1667 64 993 0.3 1 152 841 65 884 0.3 1 137 747 66 1566 0.3 1 270 1296 67 814 0.3 1 119 695 68 800 0.3 1 128 672 69 759 0.3 1 131 628 70 673 0.3 1 95 578 71 632 0.3 1 105 527 72 599 0.3 1 91 508 73 605 0.3 1 99 506 74 594 0.3 1 94 500 75 930 0.3 1 172 758 76 662 0.3 1 105 557 77 677 0.3 1 98 579 78 507 0.3 1 85 422 79 539 0.3 1 88 451 80 574 0.3 1 90 484 81 577 0.3 1 77 500 82 626 0.3 1 101 525 83 612 0.3 1 96 516 84 735 0.3 1 101 634 85 866 0.3 1 133 733 86 503 0.3 1 82 421 87 421 0.3 1 74 347 88 403 0.3 1 62 341 89 388 0.3 1 69 319 90 321 0.3 1 41 280 91 271 0.3 1 38 233 92 284 0.3 1 41 243 93 371 0.3 1 57 314 94 335 0.3 1 56 279 95 191 0.3 1 33 158 96 257 0.3 1 36 221 97 252 0.3 1 36 216 98 216 0.3 1 30 186 99 261 0.3 1 43 218 100 204 0.3 1 19 185 101 196 0.3 1 26 170 102 251 0.3 1 36 215 103 133 0.3 1 14 119 104 80 0.3 1 9 71 105 75 0.3 1 8 67 106 59 0.3 1 9 50 107 38 0.3 1 4 34 108 41 0.3 1 5 36 109 62 0.3 1 11 51 110 36 0.3 1 7 29 111 15 0.3 1 2 13 112 4 0.3 1 1 3 113 2 0.3 1 0 2 114 6 0.3 1 1 5 115 3 0.3 1 2 1 116 2 0.3 1 0 2 117 1 0.3 1 1 118 2 0.3 1 2 120 1 0.3 1 1 122 1 0.3 1 1 123 1 0.3 1 1 124 1 0.3 1 1 125 1 0.3 1 1 126 4 0.3 1 3 1 127 2 0.3 1 2 128 3 0.3 1 1 2 129 6 0.3 1 4 2 130 5 0.3 1 3 2 131 4 0.3 1 4 132 8 0.3 1 8 133 11 0.3 1 9 2 134 22 0.3 1 17 5 135 43 0.3 1 39 4 136 195 0.3 1 169 26 137 10834 0.3 1 10409 425 138 40244 0.3 1 38685 1559 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201104_20201106/RRBS20A041630_val_2.fq.gz ============================================= 18184059 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1024066 (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: 18184059 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 110861 (0.61%)