SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041686_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/20201110/tmp/caea572a-5581-11eb-b08d-6c92bfc13316/trimmed/RRBS20A041686_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 816.11 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 33,457,696 Reads with adapters: 14,016,569 (41.9%) Reads written (passing filters): 33,457,696 (100.0%) Total basepairs processed: 3,369,793,263 bp Total written (filtered): 3,299,939,261 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14016569 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.9% C: 4.2% G: 18.9% T: 46.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9798051 8364424.0 0 9798051 2 2836571 2091106.0 0 2836571 3 692748 522776.5 0 692748 4 148401 130694.1 0 148401 5 13218 32673.5 0 13218 6 9655 8168.4 0 9655 7 7743 2042.1 0 7743 8 7219 510.5 0 7219 9 8605 127.6 0 8034 571 10 8884 31.9 1 5479 3405 11 3885 8.0 1 690 3195 12 1702 2.0 1 326 1376 13 1634 0.5 1 310 1324 14 3663 0.5 1 581 3082 15 2632 0.5 1 458 2174 16 7940 0.5 1 1585 6355 17 7531 0.5 1 1222 6309 18 3118 0.5 1 627 2491 19 166 0.5 1 14 152 20 1494 0.5 1 250 1244 21 110 0.5 1 11 99 22 304 0.5 1 42 262 23 1457 0.5 1 250 1207 24 5398 0.5 1 878 4520 25 2331 0.5 1 399 1932 26 810 0.5 1 105 705 27 2075 0.5 1 343 1732 28 4119 0.5 1 657 3462 29 4545 0.5 1 710 3835 30 1146 0.5 1 209 937 31 357 0.5 1 54 303 32 2064 0.5 1 374 1690 33 3928 0.5 1 617 3311 34 4773 0.5 1 827 3946 35 2512 0.5 1 425 2087 36 1843 0.5 1 299 1544 37 3926 0.5 1 679 3247 38 748 0.5 1 116 632 39 624 0.5 1 109 515 40 2812 0.5 1 409 2403 41 1672 0.5 1 255 1417 42 3292 0.5 1 543 2749 43 5491 0.5 1 876 4615 44 909 0.5 1 112 797 45 2548 0.5 1 403 2145 46 715 0.5 1 92 623 47 1381 0.5 1 189 1192 48 4303 0.5 1 727 3576 49 510 0.5 1 65 445 50 1859 0.5 1 297 1562 51 670 0.5 1 119 551 52 552 0.5 1 78 474 53 1258 0.5 1 181 1077 54 3955 0.5 1 556 3399 55 2546 0.5 1 389 2157 56 1302 0.5 1 203 1099 57 1642 0.5 1 267 1375 58 933 0.5 1 122 811 59 554 0.5 1 85 469 60 806 0.5 1 140 666 61 1201 0.5 1 150 1051 62 4800 0.5 1 724 4076 63 847 0.5 1 136 711 64 137 0.5 1 13 124 65 114 0.5 1 10 104 66 1483 0.5 1 184 1299 67 415 0.5 1 35 380 68 1737 0.5 1 238 1499 69 2007 0.5 1 290 1717 70 3101 0.5 1 497 2604 71 661 0.5 1 85 576 72 242 0.5 1 28 214 73 816 0.5 1 91 725 74 707 0.5 1 98 609 75 1052 0.5 1 165 887 76 1086 0.5 1 166 920 77 1325 0.5 1 196 1129 78 1311 0.5 1 206 1105 79 1393 0.5 1 202 1191 80 1686 0.5 1 243 1443 81 1382 0.5 1 219 1163 82 1429 0.5 1 208 1221 83 1590 0.5 1 234 1356 84 1106 0.5 1 163 943 85 1198 0.5 1 167 1031 86 1325 0.5 1 168 1157 87 942 0.5 1 128 814 88 876 0.5 1 125 751 89 1101 0.5 1 176 925 90 894 0.5 1 145 749 91 964 0.5 1 147 817 92 760 0.5 1 100 660 93 2732 0.5 1 347 2385 94 6693 0.5 1 869 5824 95 1228 0.5 1 161 1067 96 754 0.5 1 90 664 97 5027 0.5 1 612 4415 98 824 0.5 1 115 709 99 387 0.5 1 47 340 100 386 0.5 1 62 324 101 450 0.5 1 61 389 102 942 0.5 1 181 761 103 255 0.5 1 43 212 104 176 0.5 1 22 154 105 175 0.5 1 32 143 106 146 0.5 1 26 120 107 91 0.5 1 11 80 108 33 0.5 1 5 28 109 47 0.5 1 9 38 110 52 0.5 1 14 38 111 24 0.5 1 1 23 112 15 0.5 1 5 10 113 2 0.5 1 0 2 114 10 0.5 1 4 6 115 1 0.5 1 0 1 116 1 0.5 1 1 117 4 0.5 1 2 2 118 2 0.5 1 2 120 2 0.5 1 1 1 121 4 0.5 1 3 1 122 6 0.5 1 4 2 123 1 0.5 1 0 1 124 4 0.5 1 2 2 125 4 0.5 1 2 2 126 3 0.5 1 3 127 7 0.5 1 7 128 2 0.5 1 2 129 6 0.5 1 3 3 130 8 0.5 1 8 131 10 0.5 1 7 3 132 26 0.5 1 19 7 133 69 0.5 1 44 25 134 120 0.5 1 92 28 135 81 0.5 1 62 19 136 176 0.5 1 151 25 137 7941 0.5 1 7654 287 138 300298 0.5 1 293331 6967 140 14 0.5 1 0 14 143 2 0.5 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041686_val_1.fq.gz ============================================= 33457696 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1471837 (4.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14016551 (41.9%)