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 03-Jun-2021 04:17:40 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/2_msa/P49747_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/3_mltree/P49747.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622683060 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/P49747/2_msa/P49747_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 757 sites WARNING: Sequences tr_E1C3P2_E1C3P2_CHICK_9031 and sp_P35440_TSP2_CHICK_9031 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2I3RTE4_A0A2I3RTE4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and sp_P35555_FBN1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2R9CMD1_A0A2R9CMD1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R1N5_G3R1N5_GORGO_9595 and tr_H2Q073_H2Q073_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R1N5_G3R1N5_GORGO_9595 and sp_P49746_TSP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R1N5_G3R1N5_GORGO_9595 and tr_A0A2R9CM69_A0A2R9CM69_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PFZ4_H2PFZ4_PONAB_9601 and tr_A0A2R9B1Q9_A0A2R9B1Q9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RP89_A0A2I3RP89_PANTR_9598 and tr_A0A2R8ZKW5_A0A2R8ZKW5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q1P2_H2Q1P2_PANTR_9598 and tr_A0A2R9AM34_A0A2R9AM34_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_G7PBA1_G7PBA1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A096NM08_A0A096NM08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K5L3Z1_A0A2K5L3Z1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K6BW09_A0A2K6BW09_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WIY2_F6WIY2_MACMU_9544 and tr_A0A2K6DTH7_A0A2K6DTH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZVD5_F6ZVD5_MACMU_9544 and tr_G8F669_G8F669_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZVD5_F6ZVD5_MACMU_9544 and tr_A0A2K6ECM2_A0A2K6ECM2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EPG2_F7EPG2_MACMU_9544 and tr_G7P7U6_G7P7U6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1L4Y3_G1L4Y3_AILME_9646 and tr_A0A2Y9KTV2_A0A2Y9KTV2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1L4Y3_G1L4Y3_AILME_9646 and tr_A0A384DBL5_A0A384DBL5_URSMA_29073 are exactly identical! WARNING: Sequences tr_B3S0C6_B3S0C6_TRIAD_10228 and tr_A0A369RTQ1_A0A369RTQ1_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A096N055_A0A096N055_PAPAN_9555 and tr_A0A2K5MVX6_A0A2K5MVX6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N055_A0A096N055_PAPAN_9555 and tr_A0A2K5YAW4_A0A2K5YAW4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MNL2_A0A2I3MNL2_PAPAN_9555 and tr_A0A2K5L1X0_A0A2K5L1X0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MNL2_A0A2I3MNL2_PAPAN_9555 and tr_A0A2K5Y0L4_A0A2K5Y0L4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I0MDK3_A0A2I0MDK3_COLLI_8932 and tr_A0A1V4JE24_A0A1V4JE24_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MTY5_A0A2I0MTY5_COLLI_8932 and tr_A0A1V4JKT0_A0A1V4JKT0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226MM39_A0A226MM39_CALSU_9009 and tr_A0A226P0X1_A0A226P0X1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PYK9_A0A2D0PYK9_ICTPU_7998 and tr_A0A2D0PZW0_A0A2D0PZW0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PYK9_A0A2D0PYK9_ICTPU_7998 and tr_A0A2D0PZY1_A0A2D0PZY1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L0F9_A0A2K5L0F9_CERAT_9531 and tr_A0A2K6A267_A0A2K6A267_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LWE5_A0A2K5LWE5_CERAT_9531 and tr_A0A2K5Z3D4_A0A2K5Z3D4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6B4V2_A0A2K6B4V2_MACNE_9545 and tr_A0A2K6A2Y2_A0A2K6A2Y2_MANLE_9568 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/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747.raxml.reduced.phy Alignment comprises 1 partitions and 757 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 757 Gaps: 23.44 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747.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/P49747/3_mltree/P49747.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 190 / 15200 [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: -287812.839737 [00:00:00 -287812.839737] Initial branch length optimization [00:00:02 -286264.219472] Model parameter optimization (eps = 0.100000) [00:01:21] Tree #1, final logLikelihood: -285367.070872 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.137871,0.300797) (0.122158,1.436988) (0.430476,0.698679) (0.309495,1.558103) 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/P49747/4_raxmlng_ancestral/P49747.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49747/4_raxmlng_ancestral/P49747.raxml.log Analysis started: 03-Jun-2021 04:17:40 / finished: 03-Jun-2021 04:19:08 Elapsed time: 88.356 seconds Consumed energy: 6.075 Wh