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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 01:44:06 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/2_msa/P06744_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/3_mltree/P06744.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622673846 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/020621_run/phylogeny-snakemake/results/P06744/2_msa/P06744_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 558 sites WARNING: Sequences tr_B6QD47_B6QD47_TALMQ_441960 and tr_A0A093VIC8_A0A093VIC8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WMM8_B2WMM8_PYRTR_426418 and tr_A0A317AUL1_A0A317AUL1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q28Y79_Q28Y79_DROPS_46245 and tr_B4GCU1_B4GCU1_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NBA7_B8NBA7_ASPFN_332952 and sp_Q9HGZ2_G6PI_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NBA7_B8NBA7_ASPFN_332952 and tr_A0A0F0I0T5_A0A0F0I0T5_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NBA7_B8NBA7_ASPFN_332952 and tr_A0A1S9DDH2_A0A1S9DDH2_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NBA7_B8NBA7_ASPFN_332952 and tr_A0A2G7EMT3_A0A2G7EMT3_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UTZ8_A0A179UTZ8_BLAGS_559298 and tr_C5GSB5_C5GSB5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E9F7G8_E9F7G8_METRA_655844 and tr_A0A0D9P7T9_A0A0D9P7T9_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4UTF9_J4UTF9_BEAB2_655819 and tr_A0A0A2VM31_A0A0A2VM31_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4UTF9_J4UTF9_BEAB2_655819 and tr_A0A2N6P171_A0A2N6P171_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0E0HNM5_A0A0E0HNM5_ORYNI_4536 and tr_A0A0D3GF06_A0A0D3GF06_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2R808_A2R808_ASPNC_425011 and tr_G3Y685_G3Y685_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R808_A2R808_ASPNC_425011 and tr_A0A319BXI7_A0A319BXI7_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XD03_G7XD03_ASPKW_1033177 and tr_A0A100ILW0_A0A100ILW0_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XD03_G7XD03_ASPKW_1033177 and tr_A0A146FEH4_A0A146FEH4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XD03_G7XD03_ASPKW_1033177 and tr_A0A317VAR8_A0A317VAR8_9EURO_1448314 are exactly identical! WARNING: Sequences tr_M1V5Y8_M1V5Y8_CYAM1_280699 and tr_M1V5Y9_M1V5Y9_CYAM1_280699 are exactly identical! WARNING: Sequences tr_I1Q1B2_I1Q1B2_ORYGL_4538 and sp_P42863_G6PIB_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F2SMN7_F2SMN7_TRIRC_559305 and tr_A0A178EQP8_A0A178EQP8_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XU68_A0A0D2XU68_FUSO4_426428 and tr_N4UNP1_N4UNP1_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2XU68_A0A0D2XU68_FUSO4_426428 and tr_X0DQY8_X0DQY8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XU68_A0A0D2XU68_FUSO4_426428 and tr_A0A2H3T206_A0A2H3T206_FUSOX_5507 are exactly identical! WARNING: Sequences tr_S0DWF3_S0DWF3_GIBF5_1279085 and tr_A0A365MKA9_A0A365MKA9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2XM61_V2XM61_MONRO_1381753 and tr_A0A0W0EV30_A0A0W0EV30_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RHI5_W2RHI5_PHYPN_761204 and tr_W2JSR1_W2JSR1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2I3NEH6_A0A2I3NEH6_PAPAN_9555 and tr_A0A2K5KPV5_A0A2K5KPV5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NEH6_A0A2I3NEH6_PAPAN_9555 and tr_A0A2K6C0C2_A0A2K6C0C2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0F8XU69_A0A0F8XU69_9EURO_308745 and tr_A0A2T5LQC2_A0A2T5LQC2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0G4NX34_A0A0G4NX34_PENCA_1429867 and tr_A0A101MFE4_A0A101MFE4_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0V1CMH1_A0A0V1CMH1_TRIBR_45882 and tr_A0A0V0UXH3_A0A0V0UXH3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CMH1_A0A0V1CMH1_TRIBR_45882 and tr_A0A0V0TVC0_A0A0V0TVC0_9BILA_144512 are exactly identical! WARNING: Duplicate sequences found: 32 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.raxml.reduced.phy Alignment comprises 1 partitions and 558 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 558 Gaps: 4.67 % Invariant sites: 0.90 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.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/020621_run/phylogeny-snakemake/results/P06744/3_mltree/P06744.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 140 / 11200 [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: -203659.160008 [00:00:00 -203659.160008] Initial branch length optimization [00:00:01 -203625.856933] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -203218.351963 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.249852,0.243640) (0.317246,0.444420) (0.203479,0.901681) (0.229424,2.679159) 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/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P06744/4_raxmlng_ancestral/P06744.raxml.log Analysis started: 03-Jun-2021 01:44:06 / finished: 03-Jun-2021 01:44:47 Elapsed time: 41.092 seconds Consumed energy: 2.645 Wh