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 17:36:01 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/2_msa/Q9UMS0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/3_mltree/Q9UMS0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/4_raxmlng_ancestral/Q9UMS0 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100561 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/Q9UMS0/2_msa/Q9UMS0_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 254 sites WARNING: Sequences tr_J3KEK9_J3KEK9_COCIM_246410 and tr_E9DFF2_E9DFF2_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KEK9_J3KEK9_COCIM_246410 and tr_A0A0J6YDX9_A0A0J6YDX9_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QKL6_B6QKL6_TALMQ_441960 and tr_A0A093UUJ2_A0A093UUJ2_TALMA_1077442 are exactly identical! WARNING: Sequences tr_C0NCG7_C0NCG7_AJECG_447093 and tr_C6HAS6_C6HAS6_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NCG7_C0NCG7_AJECG_447093 and tr_F0UI37_F0UI37_AJEC8_544711 are exactly identical! WARNING: Sequences sp_B5DKJ8_NFU1_DROPS_46245 and sp_B4H303_NFU1_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8N3M1_B8N3M1_ASPFN_332952 and tr_A0A2G7FLN2_A0A2G7FLN2_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UNI3_A0A179UNI3_BLAGS_559298 and tr_C5GDD2_C5GDD2_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3SGT1_A0A2I3SGT1_PANTR_9598 and tr_A0A2R9B582_A0A2R9B582_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FGS0_F9FGS0_FUSOF_660025 and tr_N4TG31_N4TG31_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FGS0_F9FGS0_FUSOF_660025 and tr_A0A2H3TBQ2_A0A2H3TBQ2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9EPY7_E9EPY7_METRA_655844 and tr_A0A0B4I6V9_A0A0B4I6V9_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EPY7_E9EPY7_METRA_655844 and tr_A0A0D9P608_A0A0D9P608_METAN_1291518 are exactly identical! WARNING: Sequences tr_J5K2H6_J5K2H6_BEAB2_655819 and tr_A0A0A2VL49_A0A0A2VL49_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A0E0H9T6_A0A0E0H9T6_ORYNI_4536 and tr_A2Y0K2_A2Y0K2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A2Q883_A2Q883_ASPNC_425011 and tr_G7XPG3_G7XPG3_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2Q883_A2Q883_ASPNC_425011 and tr_G3XRM8_G3XRM8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2Q883_A2Q883_ASPNC_425011 and tr_A0A146FNR7_A0A146FNR7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2Q883_A2Q883_ASPNC_425011 and tr_A0A318ZXD4_A0A318ZXD4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_I1PSL3_I1PSL3_ORYGL_4538 and tr_A0A0D3G3E9_A0A0D3G3E9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YCG8_G2YCG8_BOTF4_999810 and tr_M7THT0_M7THT0_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_L2FKF8_L2FKF8_COLFN_1213859 and tr_T0JMT5_T0JMT5_COLGC_1237896 are exactly identical! WARNING: Sequences tr_V2Z2H5_V2Z2H5_MONRO_1381753 and tr_A0A0W0F9S2_A0A0W0F9S2_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A3B5XVW0_A0A3B5XVW0_WHEAT_4565 and tr_A0A3B5ZQF4_A0A3B5ZQF4_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015LCE5_A0A015LCE5_9GLOM_1432141 and tr_A0A2I1DXE0_A0A2I1DXE0_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A067DGN1_A0A067DGN1_CITSI_2711 and tr_V4TJB6_V4TJB6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067DGN1_A0A067DGN1_CITSI_2711 and tr_A0A2H5PSS0_A0A2H5PSS0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078IIR8_A0A078IIR8_BRANA_3708 and tr_A0A0D3CPZ6_A0A0D3CPZ6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094E7X9_A0A094E7X9_9PEZI_1420912 and tr_A0A1B8GG17_A0A1B8GG17_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A0KE63_A0A0A0KE63_CUCSA_3659 and tr_A0A1S4E1X6_A0A1S4E1X6_CUCME_3656 are exactly identical! WARNING: Sequences tr_A0A0D2UWA7_A0A0D2UWA7_GOSRA_29730 and tr_A0A1U8JCJ8_A0A1U8JCJ8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0A1NBG3_A0A0A1NBG3_9FUNG_58291 and tr_A0A367J5N0_A0A367J5N0_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A117DW45_A0A117DW45_ASPNG_5061 and tr_A0A1L9NCV8_A0A1L9NCV8_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A2H3E4X9_A0A2H3E4X9_ARMGA_47427 and tr_A0A2H3C3F3_A0A2H3C3F3_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2K5MTF2_A0A2K5MTF2_CERAT_9531 and tr_A0A2K5Z5N7_A0A2K5Z5N7_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 35 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/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.raxml.reduced.phy Alignment comprises 1 partitions and 254 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 254 Gaps: 14.30 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.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/Q9UMS0/3_mltree/Q9UMS0.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 64 / 5120 [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: -119035.704164 [00:00:00 -119035.704164] Initial branch length optimization [00:00:01 -117518.032334] Model parameter optimization (eps = 0.100000) [00:00:39] Tree #1, final logLikelihood: -117191.972334 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.271527,0.252953) (0.188018,0.394029) (0.231774,0.835718) (0.308682,2.149573) 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/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UMS0/4_raxmlng_ancestral/Q9UMS0.raxml.log Analysis started: 12-Jul-2021 17:36:01 / finished: 12-Jul-2021 17:36:43 Elapsed time: 41.700 seconds Consumed energy: 3.764 Wh