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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:35:40 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/2_msa/Q9NY28_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/3_mltree/Q9NY28.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802940 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/2_msa/Q9NY28_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 637 sites WARNING: Sequences tr_Q5ZJL1_Q5ZJL1_CHICK_9031 and tr_G1N4F1_G1N4F1_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q5ZJL1_Q5ZJL1_CHICK_9031 and tr_R0KTZ1_R0KTZ1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q5ZJL1_Q5ZJL1_CHICK_9031 and tr_A0A091G724_A0A091G724_9AVES_55661 are exactly identical! WARNING: Sequences tr_M3XPY0_M3XPY0_MUSPF_9669 and tr_A0A2Y9ITF4_A0A2Y9ITF4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q6WV17_GALT5_DROME_7227 and tr_B4I1D1_B4I1D1_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_H2QEF9_H2QEF9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and sp_Q10472_GALT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A1D5QKP2_A0A1D5QKP2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_G7PWN3_G7PWN3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A0D9RZ91_A0A0D9RZ91_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A2K5LHK4_A0A2K5LHK4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A2K6E780_A0A2K6E780_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A2K5Z9Y0_A0A2K5Z9Y0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R326_G1R326_NOMLE_61853 and tr_A0A2R8ZP22_A0A2R8ZP22_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RKZ0_G1RKZ0_NOMLE_61853 and tr_A0A2I3S6E4_A0A2I3S6E4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QSQ1_G3QSQ1_GORGO_9595 and sp_Q6IS24_GLT17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QSQ1_G3QSQ1_GORGO_9595 and tr_F6Y9A8_F6Y9A8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QSQ1_G3QSQ1_GORGO_9595 and tr_A0A096NFF7_A0A096NFF7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2P7K5_H2P7K5_PONAB_9601 and sp_Q8IUC8_GLT13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P7K5_H2P7K5_PONAB_9601 and tr_A0A2R9B4U5_A0A2R9B4U5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1TU10_G1TU10_RABIT_9986 and tr_I3MHQ1_I3MHQ1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_Q292V0_Q292V0_DROPS_46245 and tr_B4GCL2_B4GCL2_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RM54_E2RM54_CANLF_9615 and tr_G1L0P3_G1L0P3_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RM54_E2RM54_CANLF_9615 and tr_A0A384C4Z7_A0A384C4Z7_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2Q369_H2Q369_PANTR_9598 and sp_Q6P9A2_GLT18_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q369_H2Q369_PANTR_9598 and tr_A0A2R9C0Y9_A0A2R9C0Y9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K6ZCD8_K6ZCD8_PANTR_9598 and tr_A0A2R9AQX0_A0A2R9AQX0_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P6I9_W5P6I9_SHEEP_9940 and tr_M3WYS9_M3WYS9_FELCA_9685 are exactly identical! WARNING: Sequences tr_W5P6I9_W5P6I9_SHEEP_9940 and tr_A0A2Y9PJ44_A0A2Y9PJ44_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5P6I9_W5P6I9_SHEEP_9940 and tr_A0A2Y9FCN4_A0A2Y9FCN4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A158NQJ6_A0A158NQJ6_ATTCE_12957 and tr_A0A195BR02_A0A195BR02_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6S0F0_F6S0F0_MACMU_9544 and tr_A0A2K6B4W8_A0A2K6B4W8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZCJ7_H0ZCJ7_TAEGU_59729 and tr_A0A093PC30_A0A093PC30_9PASS_328815 are exactly identical! WARNING: Sequences tr_G7P233_G7P233_MACFA_9541 and tr_A0A2K6AQI0_A0A2K6AQI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PQQ2_G7PQQ2_MACFA_9541 and tr_A0A096NRX7_A0A096NRX7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PQQ2_G7PQQ2_MACFA_9541 and tr_A0A2K5KMM9_A0A2K5KMM9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091JZ52_A0A091JZ52_EGRGA_188379 and tr_A0A091UPP7_A0A091UPP7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091V0C0_A0A091V0C0_NIPNI_128390 and tr_R7VTU8_R7VTU8_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A087QSL6_A0A087QSL6_APTFO_9233 and tr_A0A0A0AQH7_A0A0A0AQH7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087R6V7_A0A087R6V7_APTFO_9233 and tr_A0A0A0AU94_A0A0A0AU94_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1D5R8_A0A0V1D5R8_TRIBR_45882 and tr_A0A0V0TEW4_A0A0V0TEW4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0USB2_A0A0V0USB2_9BILA_181606 and tr_A0A0V1PAN4_A0A0V1PAN4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1LWC8_A0A0V1LWC8_9BILA_6335 and tr_A0A0V0TYV7_A0A0V0TYV7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1M9T6_A0A0V1M9T6_9BILA_268474 and tr_A0A0V1I8C6_A0A0V1I8C6_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A2U4AA85_A0A2U4AA85_TURTR_9739 and tr_A0A2Y9N883_A0A2Y9N883_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 45 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.raxml.reduced.phy Alignment comprises 1 partitions and 637 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 637 Gaps: 20.07 % Invariant sites: 0.94 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/3_mltree/Q9NY28.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 160 / 12800 [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: -227312.372055 [00:00:00 -227312.372055] Initial branch length optimization [00:00:01 -213382.698346] Model parameter optimization (eps = 0.100000) [00:00:36] Tree #1, final logLikelihood: -213027.898612 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.124128,0.175716) (0.198452,0.271459) (0.334979,0.827215) (0.342441,1.890009) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9NY28/4_raxmlng_ancestral/Q9NY28.raxml.log Analysis started: 04-Jun-2021 13:35:40 / finished: 04-Jun-2021 13:36:22 Elapsed time: 41.860 seconds