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 15-Jul-2021 23:53:34 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/2_msa/Q13029_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/3_mltree/Q13029.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/4_raxmlng_ancestral/Q13029 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626382414 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/Q13029/2_msa/Q13029_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1718 sites WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_U3JFF3_U3JFF3_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A1V4J6C7_A0A1V4J6C7_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A218V159_A0A218V159_9PASE_299123 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226NP02_A0A226NP02_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226P0G4_A0A226P0G4_COLVI_9014 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_D3ZEJ0_D3ZEJ0_RAT_10116 are exactly identical! WARNING: Sequences tr_G1RPQ6_G1RPQ6_NOMLE_61853 and tr_A0A2K5Z9L2_A0A2K5Z9L2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ZNF0_A0A2I2ZNF0_GORGO_9595 and tr_H2PE77_H2PE77_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZNF0_A0A2I2ZNF0_GORGO_9595 and sp_Q9NQX1_PRDM5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QHR5_G3QHR5_GORGO_9595 and tr_H2QTH1_H2QTH1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QHR5_G3QHR5_GORGO_9595 and tr_A0A2R8ZUJ0_A0A2R8ZUJ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R6V8_G3R6V8_GORGO_9595 and tr_H2PQI9_H2PQI9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R6V8_G3R6V8_GORGO_9595 and tr_H2QWA1_H2QWA1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6V8_G3R6V8_GORGO_9595 and sp_Q9GZV8_PRD14_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6V8_G3R6V8_GORGO_9595 and tr_A0A2R8ZS07_A0A2R8ZS07_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S4A4_G3S4A4_GORGO_9595 and tr_H2QY20_H2QY20_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S4A4_G3S4A4_GORGO_9595 and sp_Q9H4Q4_PRD12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1NLB4_G1NLB4_MELGA_9103 and tr_A0A226NJT3_A0A226NJT3_CALSU_9009 are exactly identical! WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and sp_Q9NQX0_PRDM6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and tr_A0A2I3MF44_A0A2I3MF44_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and tr_A0A0D9RQ11_A0A0D9RQ11_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and tr_A0A2K5LQI9_A0A2K5LQI9_CERAT_9531 are exactly identical! WARNING: Sequences tr_W5QC25_W5QC25_SHEEP_9940 and sp_A6QPM3_PRDM6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_I3M7W1_I3M7W1_ICTTR_43179 and tr_F1RKP0_F1RKP0_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A0H5S6I3_A0A0H5S6I3_BRUMA_6279 and tr_A0A0N4TUV9_A0A0N4TUV9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F6VYT2_F6VYT2_MACMU_9544 and tr_A0A2K5ZG20_A0A2K5ZG20_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FD48_F7FD48_MACMU_9544 and tr_G7P449_G7P449_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FD48_F7FD48_MACMU_9544 and tr_A0A096MQB7_A0A096MQB7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F1S0X7_F1S0X7_PIG_9823 and tr_A0A337SEE4_A0A337SEE4_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A096N3I7_A0A096N3I7_PAPAN_9555 and tr_A0A2K5LE40_A0A2K5LE40_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N3I7_A0A096N3I7_PAPAN_9555 and tr_A0A2K5XVZ4_A0A2K5XVZ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N5L8_A0A096N5L8_PAPAN_9555 and tr_A0A2K6AY75_A0A2K6AY75_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096P0F9_A0A096P0F9_PAPAN_9555 and tr_A0A0D9RQI6_A0A0D9RQI6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P0F9_A0A096P0F9_PAPAN_9555 and tr_A0A2K5L0P9_A0A2K5L0P9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P0F9_A0A096P0F9_PAPAN_9555 and tr_A0A2K6CVC9_A0A2K6CVC9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151MFL3_A0A151MFL3_ALLMI_8496 and tr_A0A1U7RR30_A0A1U7RR30_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JR11_A0A091JR11_EGRGA_188379 and tr_A0A093I2Y2_A0A093I2Y2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A0A0B4P0_A0A0A0B4P0_CHAVO_50402 and tr_A0A093GL40_A0A093GL40_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0A0B4P0_A0A0A0B4P0_CHAVO_50402 and tr_A0A091HVF6_A0A091HVF6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2D0QW48_A0A2D0QW48_ICTPU_7998 and tr_A0A2D0QWG6_A0A2D0QWG6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R6H2_A0A2D0R6H2_ICTPU_7998 and tr_A0A2D0R6J8_A0A2D0R6J8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R6H2_A0A2D0R6H2_ICTPU_7998 and tr_A0A2D0R813_A0A2D0R813_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R6H2_A0A2D0R6H2_ICTPU_7998 and tr_A0A2D0R8P5_A0A2D0R8P5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9PBU0_A0A2Y9PBU0_DELLE_9749 and tr_A0A2Y9SU42_A0A2Y9SU42_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 44 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/Q13029/4_raxmlng_ancestral/Q13029.raxml.reduced.phy Alignment comprises 1 partitions and 1718 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1718 Gaps: 68.66 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/4_raxmlng_ancestral/Q13029.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/Q13029/3_mltree/Q13029.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 430 / 34400 [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: -602547.697171 [00:00:00 -602547.697171] Initial branch length optimization [00:00:07 -394534.980614] Model parameter optimization (eps = 0.100000) [00:04:38] Tree #1, final logLikelihood: -392120.860607 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.124392,0.417085) (0.119978,1.176403) (0.319161,0.655905) (0.436468,1.369253) 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/Q13029/4_raxmlng_ancestral/Q13029.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/4_raxmlng_ancestral/Q13029.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/4_raxmlng_ancestral/Q13029.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13029/4_raxmlng_ancestral/Q13029.raxml.log Analysis started: 15-Jul-2021 23:53:34 / finished: 15-Jul-2021 23:58:30 Elapsed time: 295.579 seconds Consumed energy: 25.123 Wh