SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041629_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/a593f6f2-5572-11eb-abe2-6c92bfc1231a/trimmed/RRBS20A041629_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 769.84 s (21 us/read; 2.84 M reads/minute). === Summary === Total reads processed: 36,466,929 Reads with adapters: 15,851,942 (43.5%) Reads written (passing filters): 36,466,929 (100.0%) Total basepairs processed: 3,648,612,480 bp Total written (filtered): 3,441,032,266 bp (94.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15851942 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 0.5% G: 19.1% T: 50.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10653064 9116732.2 0 10653064 2 2822060 2279183.1 0 2822060 3 725134 569795.8 0 725134 4 168304 142448.9 0 168304 5 10885 35612.2 0 10885 6 6987 8903.1 0 6987 7 6026 2225.8 0 6026 8 4528 556.4 0 4528 9 5351 139.1 0 4793 558 10 6646 34.8 1 3276 3370 11 2758 8.7 1 325 2433 12 1305 2.2 1 145 1160 13 1237 0.5 1 148 1089 14 2116 0.5 1 263 1853 15 1522 0.5 1 199 1323 16 3535 0.5 1 337 3198 17 4389 0.5 1 550 3839 18 3037 0.5 1 879 2158 19 200 0.5 1 17 183 20 1067 0.5 1 156 911 21 156 0.5 1 15 141 22 260 0.5 1 35 225 23 1149 0.5 1 128 1021 24 3549 0.5 1 441 3108 25 1523 0.5 1 223 1300 26 635 0.5 1 95 540 27 1679 0.5 1 192 1487 28 3038 0.5 1 350 2688 29 3051 0.5 1 369 2682 30 928 0.5 1 148 780 31 195 0.5 1 23 172 32 1312 0.5 1 173 1139 33 2221 0.5 1 265 1956 34 2100 0.5 1 277 1823 35 3361 0.5 1 370 2991 36 1570 0.5 1 160 1410 37 939 0.5 1 122 817 38 2211 0.5 1 273 1938 39 1168 0.5 1 149 1019 40 2898 0.5 1 286 2612 41 2447 0.5 1 289 2158 42 2266 0.5 1 229 2037 43 3204 0.5 1 317 2887 44 602 0.5 1 50 552 45 1613 0.5 1 186 1427 46 703 0.5 1 72 631 47 1233 0.5 1 135 1098 48 3370 0.5 1 356 3014 49 404 0.5 1 33 371 50 1298 0.5 1 140 1158 51 563 0.5 1 54 509 52 489 0.5 1 32 457 53 1073 0.5 1 105 968 54 2833 0.5 1 324 2509 55 2238 0.5 1 286 1952 56 1442 0.5 1 177 1265 57 1445 0.5 1 203 1242 58 1035 0.5 1 130 905 59 586 0.5 1 57 529 60 950 0.5 1 98 852 61 1379 0.5 1 148 1231 62 3462 0.5 1 500 2962 63 984 0.5 1 144 840 64 209 0.5 1 29 180 65 157 0.5 1 32 125 66 553 0.5 1 93 460 67 447 0.5 1 48 399 68 1518 0.5 1 193 1325 69 1786 0.5 1 217 1569 70 2944 0.5 1 317 2627 71 1235 0.5 1 125 1110 72 552 0.5 1 59 493 73 641 0.5 1 64 577 74 668 0.5 1 76 592 75 882 0.5 1 103 779 76 839 0.5 1 97 742 77 862 0.5 1 80 782 78 894 0.5 1 74 820 79 860 0.5 1 97 763 80 992 0.5 1 90 902 81 756 0.5 1 82 674 82 853 0.5 1 64 789 83 967 0.5 1 122 845 84 801 0.5 1 88 713 85 1007 0.5 1 104 903 86 620 0.5 1 72 548 87 549 0.5 1 71 478 88 520 0.5 1 48 472 89 599 0.5 1 63 536 90 582 0.5 1 69 513 91 496 0.5 1 57 439 92 441 0.5 1 50 391 93 712 0.5 1 62 650 94 759 0.5 1 58 701 95 401 0.5 1 44 357 96 325 0.5 1 35 290 97 615 0.5 1 60 555 98 289 0.5 1 44 245 99 195 0.5 1 24 171 100 195 0.5 1 23 172 101 211 0.5 1 27 184 102 265 0.5 1 32 233 103 146 0.5 1 22 124 104 124 0.5 1 18 106 105 94 0.5 1 10 84 106 101 0.5 1 18 83 107 50 0.5 1 11 39 108 48 0.5 1 11 37 109 37 0.5 1 9 28 110 53 0.5 1 17 36 111 25 0.5 1 13 12 112 26 0.5 1 14 12 113 7 0.5 1 4 3 114 16 0.5 1 8 8 115 8 0.5 1 7 1 116 11 0.5 1 9 2 117 17 0.5 1 12 5 118 16 0.5 1 11 5 119 13 0.5 1 9 4 120 13 0.5 1 8 5 121 15 0.5 1 10 5 122 18 0.5 1 15 3 123 16 0.5 1 9 7 124 14 0.5 1 10 4 125 16 0.5 1 11 5 126 27 0.5 1 21 6 127 30 0.5 1 20 10 128 32 0.5 1 26 6 129 40 0.5 1 33 7 130 40 0.5 1 27 13 131 66 0.5 1 47 19 132 75 0.5 1 50 25 133 260 0.5 1 181 79 134 369 0.5 1 278 91 135 445 0.5 1 348 97 136 658 0.5 1 536 122 137 7769 0.5 1 7029 740 138 1313327 0.5 1 1274930 38397 140 9 0.5 1 0 9 141 1 0.5 1 1 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041629_val_1.fq.gz ============================================= 36466929 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1287658 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 15851939 (43.5%)