SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041628_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/c91a8e10-5581-11eb-8c95-6c92bfc39756/trimmed/RRBS20A041628_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 949.76 s (25 us/read; 2.39 M reads/minute). === Summary === Total reads processed: 37,837,628 Reads with adapters: 16,099,441 (42.5%) Reads written (passing filters): 37,837,628 (100.0%) Total basepairs processed: 3,786,346,293 bp Total written (filtered): 3,668,145,569 bp (96.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16099441 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 0.9% G: 22.5% T: 46.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11349444 9459407.0 0 11349444 2 2985927 2364851.8 0 2985927 3 694439 591212.9 0 694439 4 157459 147803.2 0 157459 5 8922 36950.8 0 8922 6 4251 9237.7 0 4251 7 3150 2309.4 0 3150 8 2801 577.4 0 2801 9 5081 144.3 0 4689 392 10 4037 36.1 1 1374 2663 11 6140 9.0 1 832 5308 12 1555 2.3 1 197 1358 13 2038 0.6 1 329 1709 14 4685 0.6 1 597 4088 15 2997 0.6 1 401 2596 16 11686 0.6 1 1376 10310 17 12079 0.6 1 2571 9508 18 7226 0.6 1 4659 2567 19 181 0.6 1 46 135 20 2096 0.6 1 378 1718 21 211 0.6 1 20 191 22 311 0.6 1 45 266 23 1808 0.6 1 215 1593 24 8393 0.6 1 1141 7252 25 3026 0.6 1 439 2587 26 1192 0.6 1 152 1040 27 2166 0.6 1 308 1858 28 5597 0.6 1 960 4637 29 6844 0.6 1 930 5914 30 855 0.6 1 140 715 31 336 0.6 1 34 302 32 2126 0.6 1 324 1802 33 4498 0.6 1 533 3965 34 5593 0.6 1 796 4797 35 2196 0.6 1 312 1884 36 2501 0.6 1 385 2116 37 6024 0.6 1 944 5080 38 2054 0.6 1 569 1485 39 844 0.6 1 143 701 40 6059 0.6 1 852 5207 41 2701 0.6 1 368 2333 42 6451 0.6 1 963 5488 43 11315 0.6 1 1618 9697 44 1607 0.6 1 177 1430 45 4037 0.6 1 583 3454 46 799 0.6 1 85 714 47 2245 0.6 1 297 1948 48 6434 0.6 1 904 5530 49 718 0.6 1 95 623 50 3779 0.6 1 519 3260 51 1174 0.6 1 145 1029 52 597 0.6 1 65 532 53 1771 0.6 1 245 1526 54 6990 0.6 1 1133 5857 55 2870 0.6 1 440 2430 56 1672 0.6 1 203 1469 57 2836 0.6 1 471 2365 58 1139 0.6 1 164 975 59 1025 0.6 1 131 894 60 1395 0.6 1 220 1175 61 1784 0.6 1 233 1551 62 9443 0.6 1 1415 8028 63 1622 0.6 1 280 1342 64 177 0.6 1 14 163 65 108 0.6 1 10 98 66 2449 0.6 1 343 2106 67 623 0.6 1 68 555 68 2874 0.6 1 384 2490 69 3428 0.6 1 489 2939 70 6946 0.6 1 979 5967 71 1690 0.6 1 220 1470 72 395 0.6 1 42 353 73 978 0.6 1 116 862 74 1029 0.6 1 147 882 75 1517 0.6 1 229 1288 76 1890 0.6 1 282 1608 77 2502 0.6 1 376 2126 78 2208 0.6 1 282 1926 79 2001 0.6 1 306 1695 80 2828 0.6 1 393 2435 81 2358 0.6 1 365 1993 82 2588 0.6 1 352 2236 83 2977 0.6 1 404 2573 84 2607 0.6 1 410 2197 85 3032 0.6 1 472 2560 86 2229 0.6 1 280 1949 87 1512 0.6 1 208 1304 88 1479 0.6 1 213 1266 89 1776 0.6 1 296 1480 90 1447 0.6 1 199 1248 91 1276 0.6 1 155 1121 92 1179 0.6 1 141 1038 93 3097 0.6 1 365 2732 94 8202 0.6 1 900 7302 95 1646 0.6 1 190 1456 96 1208 0.6 1 160 1048 97 6583 0.6 1 813 5770 98 1210 0.6 1 171 1039 99 713 0.6 1 107 606 100 658 0.6 1 94 564 101 684 0.6 1 92 592 102 1293 0.6 1 247 1046 103 505 0.6 1 76 429 104 262 0.6 1 30 232 105 222 0.6 1 34 188 106 209 0.6 1 31 178 107 120 0.6 1 13 107 108 47 0.6 1 6 41 109 54 0.6 1 9 45 110 30 0.6 1 8 22 111 23 0.6 1 3 20 112 4 0.6 1 4 113 1 0.6 1 1 114 3 0.6 1 2 1 115 1 0.6 1 0 1 116 6 0.6 1 0 6 117 1 0.6 1 0 1 118 1 0.6 1 0 1 119 1 0.6 1 1 120 3 0.6 1 2 1 121 8 0.6 1 6 2 122 9 0.6 1 7 2 123 6 0.6 1 4 2 124 7 0.6 1 4 3 125 11 0.6 1 9 2 126 12 0.6 1 11 1 127 11 0.6 1 11 128 10 0.6 1 7 3 129 22 0.6 1 18 4 130 10 0.6 1 7 3 131 19 0.6 1 16 3 132 43 0.6 1 31 12 133 111 0.6 1 73 38 134 177 0.6 1 144 33 135 155 0.6 1 128 27 136 441 0.6 1 407 34 137 39920 0.6 1 38935 985 138 570337 0.6 1 557655 12682 140 10 0.6 1 0 10 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201110/RRBS20A041628_val_1.fq.gz ============================================= 37837628 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1412136 (3.7%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16099438 (42.5%)