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 17:45:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/2_msa/Q86UP8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/3_mltree/Q86UP8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/4_raxmlng_ancestral/Q86UP8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101124 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/Q86UP8/2_msa/Q86UP8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 949 sites WARNING: Fully undetermined sequences found: 2 WARNING: Sequences tr_G1RBS1_G1RBS1_NOMLE_61853 and tr_H2PLW5_H2PLW5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RBS1_G1RBS1_NOMLE_61853 and tr_H2QUR5_H2QUR5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RBS1_G1RBS1_NOMLE_61853 and sp_P78347_GTF2I_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RBS1_G1RBS1_NOMLE_61853 and tr_A0A2R9AXQ0_A0A2R9AXQ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PZY5_G1PZY5_MYOLU_59463 and tr_G1Q7Y9_G1Q7Y9_MYOLU_59463 are exactly identical! WARNING: Sequences tr_F6Y258_F6Y258_CANLF_9615 and tr_A0A2U3VV04_A0A2U3VV04_ODORO_9708 are exactly identical! WARNING: Sequences tr_E5SDX2_E5SDX2_TRISP_6334 and tr_E5SGQ7_E5SGQ7_TRISP_6334 are exactly identical! WARNING: Sequences tr_E5T3B0_E5T3B0_TRISP_6334 and tr_A0A0V0XEI7_A0A0V0XEI7_TRIPS_6337 are exactly identical! WARNING: Sequences tr_E5T7W9_E5T7W9_TRISP_6334 and tr_E5T803_E5T803_TRISP_6334 are exactly identical! WARNING: Sequences tr_K7F6G9_K7F6G9_PELSI_13735 and tr_K7FAL6_K7FAL6_PELSI_13735 are exactly identical! WARNING: Sequences tr_K7F6G9_K7F6G9_PELSI_13735 and tr_K7FDQ2_K7FDQ2_PELSI_13735 are exactly identical! WARNING: Sequences tr_K7F6G9_K7F6G9_PELSI_13735 and tr_K7FNB8_K7FNB8_PELSI_13735 are exactly identical! WARNING: Sequences tr_K7F6G9_K7F6G9_PELSI_13735 and tr_K7FQ84_K7FQ84_PELSI_13735 are exactly identical! WARNING: Sequences tr_K7F6G9_K7F6G9_PELSI_13735 and tr_K7GDH0_K7GDH0_PELSI_13735 are exactly identical! WARNING: Sequences tr_K7FDF5_K7FDF5_PELSI_13735 and tr_K7G1U3_K7G1U3_PELSI_13735 are exactly identical! WARNING: Sequences tr_G7P185_G7P185_MACFA_9541 and tr_A0A096N5F9_A0A096N5F9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_R7TMU1_R7TMU1_CAPTE_283909 and tr_R7U160_R7U160_CAPTE_283909 are exactly identical! WARNING: Sequences tr_R7TMU1_R7TMU1_CAPTE_283909 and tr_R7VEH9_R7VEH9_CAPTE_283909 are exactly identical! WARNING: Sequences tr_A0A151N5H5_A0A151N5H5_ALLMI_8496 and tr_A0A3Q0GWP2_A0A3Q0GWP2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087T5H8_A0A087T5H8_9ARAC_407821 and tr_A0A087U0U2_A0A087U0U2_9ARAC_407821 are exactly identical! WARNING: Sequences tr_A0A087T5H8_A0A087T5H8_9ARAC_407821 and tr_A0A087U850_A0A087U850_9ARAC_407821 are exactly identical! WARNING: Sequences tr_A0A0V1C7A9_A0A0V1C7A9_TRIBR_45882 and tr_A0A0V0UL65_A0A0V0UL65_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0W1Q9_A0A0V0W1Q9_9BILA_92179 and tr_A0A0V1LQQ6_A0A0V1LQQ6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2D0QCT0_A0A2D0QCT0_ICTPU_7998 and tr_A0A2D0QFG0_A0A2D0QFG0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2J7PBR0_A0A2J7PBR0_9NEOP_105785 and tr_A0A2J7PTB9_A0A2J7PTB9_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7PBR0_A0A2J7PBR0_9NEOP_105785 and tr_A0A2J7Q5R5_A0A2J7Q5R5_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7PSG6_A0A2J7PSG6_9NEOP_105785 and tr_A0A2J7Q662_A0A2J7Q662_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7PSG6_A0A2J7PSG6_9NEOP_105785 and tr_A0A2J7Q7J4_A0A2J7Q7J4_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7PSG6_A0A2J7PSG6_9NEOP_105785 and tr_A0A2J7R0L9_A0A2J7R0L9_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7Q3W3_A0A2J7Q3W3_9NEOP_105785 and tr_A0A2J7QGG7_A0A2J7QGG7_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7QII8_A0A2J7QII8_9NEOP_105785 and tr_A0A2J7QS42_A0A2J7QS42_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7QII8_A0A2J7QII8_9NEOP_105785 and tr_A0A2J7R7G2_A0A2J7R7G2_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A2J7RD72_A0A2J7RD72_9NEOP_105785 and tr_A0A2J7RJS1_A0A2J7RJS1_9NEOP_105785 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q86UP8/4_raxmlng_ancestral/Q86UP8.raxml.reduced.phy Alignment comprises 1 partitions and 949 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 949 Gaps: 75.34 % Invariant sites: 3.16 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/4_raxmlng_ancestral/Q86UP8.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/Q86UP8/3_mltree/Q86UP8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 238 / 19040 [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: -148162.910498 [00:00:00 -148162.910498] Initial branch length optimization [00:00:35 -145319.918945] Model parameter optimization (eps = 0.100000) [00:03:57] Tree #1, final logLikelihood: -144464.017148 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.135876,0.742711) (0.082543,1.467168) (0.396139,0.689348) (0.385442,1.309929) 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/Q86UP8/4_raxmlng_ancestral/Q86UP8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/4_raxmlng_ancestral/Q86UP8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/4_raxmlng_ancestral/Q86UP8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86UP8/4_raxmlng_ancestral/Q86UP8.raxml.log Analysis started: 12-Jul-2021 17:45:24 / finished: 12-Jul-2021 17:49:41 Elapsed time: 256.681 seconds Consumed energy: 21.615 Wh