RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 17:47:15 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/2_msa/O94822_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101235 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/2_msa/O94822_nogap_msa.fasta [00:00:00] Loaded alignment with 816 taxa and 1766 sites WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_A2X8C1_A2X8C1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A2XR03_A2XR03_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_I1PJL7_I1PJL7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0E0DBR5_A0A0E0DBR5_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0E0P6A8_A0A0E0P6A8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D3FTC8_A0A0D3FTC8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D9ZHS7_A0A0D9ZHS7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_Q7XT61_Q7XT61_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A2XWQ7_A2XWQ7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A0A0E0DHK1_A0A0E0DHK1_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A0A0E0PD43_A0A0E0PD43_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_Q7XQ70_Q7XQ70_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H564_A0A0E0H564_ORYNI_4536 and tr_A0A0E0PD90_A0A0E0PD90_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H564_A0A0E0H564_ORYNI_4536 and tr_A0A0D9ZPU0_A0A0D9ZPU0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1P348_I1P348_ORYGL_4538 and tr_A0A0E0CPU0_A0A0E0CPU0_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1P348_I1P348_ORYGL_4538 and tr_A0A0E0NJ93_A0A0E0NJ93_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1P348_I1P348_ORYGL_4538 and tr_A0A0D9YWH0_A0A0D9YWH0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1P348_I1P348_ORYGL_4538 and tr_Q6EPN1_Q6EPN1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_M4FAD7_M4FAD7_BRARP_51351 and tr_A0A078JHE4_A0A078JHE4_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2QVZ6_W2QVZ6_PHYPN_761204 and tr_A0A0W8B4U4_A0A0W8B4U4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A078J4X7_A0A078J4X7_BRANA_3708 and tr_A0A0D3DM43_A0A0D3DM43_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JAG8_A0A078JAG8_BRANA_3708 and tr_A0A0D3CJI2_A0A0D3CJI2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JC68_A0A078JC68_BRANA_3708 and tr_A0A0D3BNH2_A0A0D3BNH2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A1S3X9B1_A0A1S3X9B1_TOBAC_4097 and tr_A0A1U7WM19_A0A1U7WM19_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1S3XJS4_A0A1S3XJS4_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1J6IX31_A0A1J6IX31_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1U7YCD9_A0A1U7YCD9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CUW4_A0A1S4CUW4_TOBAC_4097 and tr_A0A1U7YX35_A0A1U7YX35_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q9FQZ7_Q9FQZ7_TOBAC_4097 and tr_A0A1U7YB59_A0A1U7YB59_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A251S4V8_A0A251S4V8_HELAN_4232 and tr_A0A251S5C4_A0A251S5C4_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A251TND3_A0A251TND3_HELAN_4232 and tr_A0A251TPD5_A0A251TPD5_HELAN_4232 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.reduced.phy Alignment comprises 1 partitions and 1766 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1766 Gaps: 51.58 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 442 / 35360 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -830591.893845 [00:00:00 -830591.893845] Initial branch length optimization [00:00:03 -784266.342097] Model parameter optimization (eps = 0.100000) [00:02:01] Tree #1, final logLikelihood: -782601.940566 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.079482,0.408845) (0.115114,0.505113) (0.393549,0.737483) (0.411855,1.503255) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/4_raxmlng_ancestral/O94822.raxml.log Analysis started: 12-Jul-2021 17:47:15 / finished: 12-Jul-2021 17:49:29 Elapsed time: 133.612 seconds Consumed energy: 9.236 Wh