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 19-Jul-2021 13:45:01 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/2_msa/Q9UNN4_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/3_mltree/Q9UNN4.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626691501 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_300621/phylogeny-snakemake/results/Q9UNN4/2_msa/Q9UNN4_nogap_msa.fasta [00:00:00] Loaded alignment with 841 taxa and 478 sites WARNING: Sequences tr_M3YB68_M3YB68_MUSPF_9669 and tr_G1L572_G1L572_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YB68_M3YB68_MUSPF_9669 and tr_A0A2Y9JKK1_A0A2Y9JKK1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A0E1S2P4_A0A0E1S2P4_COCIM_246410 and tr_A0A0J6YK16_A0A0J6YK16_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QAX6_B6QAX6_TALMQ_441960 and tr_A0A093VF82_A0A093VF82_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_H2NLY7_H2NLY7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and sp_P52655_TF2AA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_F7H5J8_F7H5J8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A096NRB8_A0A096NRB8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A0D9RGW3_A0A0D9RGW3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A2K5P1M3_A0A2K5P1M3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A2K6AX07_A0A2K6AX07_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A2K5Y8M6_A0A2K5Y8M6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QL68_G3QL68_GORGO_9595 and tr_A0A2R9BJ75_A0A2R9BJ75_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8N3Z4_B8N3Z4_ASPFN_332952 and tr_Q2UL91_Q2UL91_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N3Z4_B8N3Z4_ASPFN_332952 and tr_A0A1S9DMW7_A0A1S9DMW7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_W5NY55_W5NY55_SHEEP_9940 and tr_F1MII0_F1MII0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_J5JYD9_J5JYD9_BEAB2_655819 and tr_A0A0A2VWQ1_A0A0A2VWQ1_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A158NUK7_A0A158NUK7_ATTCE_12957 and tr_A0A195BFB8_A0A195BFB8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0HC02_A0A0E0HC02_ORYNI_4536 and tr_A2Y2S6_A2Y2S6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HC02_A0A0E0HC02_ORYNI_4536 and tr_A0A0D3G5K0_A0A0D3G5K0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HC02_A0A0E0HC02_ORYNI_4536 and tr_Q0DJF8_Q0DJF8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7XIC6_G7XIC6_ASPKW_1033177 and tr_A0A117DW75_A0A117DW75_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XIC6_G7XIC6_ASPKW_1033177 and tr_A0A146FB88_A0A146FB88_9EURO_1069201 are exactly identical! WARNING: Sequences tr_E5S2I3_E5S2I3_TRISP_6334 and tr_A0A0V0S4X2_A0A0V0S4X2_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5S2I3_E5S2I3_TRISP_6334 and tr_A0A0V0U5N2_A0A0V0U5N2_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0ZQ55_H0ZQ55_TAEGU_59729 and tr_A0A218VE04_A0A218VE04_9PASE_299123 are exactly identical! WARNING: Sequences tr_E6RG06_E6RG06_CRYGW_367775 and tr_A0A095CFS3_A0A095CFS3_CRYGR_294750 are exactly identical! WARNING: Sequences tr_A0A0E0PK66_A0A0E0PK66_ORYRU_4529 and tr_A0A0D9ZWS9_A0A0D9ZWS9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F2SX09_F2SX09_TRIRC_559305 and tr_A0A178F9Y3_A0A178F9Y3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0F0IG73_A0A0F0IG73_ASPPU_1403190 and tr_A0A2G7FIH7_A0A2G7FIH7_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A151M5G2_A0A151M5G2_ALLMI_8496 and tr_A0A3Q0FYN1_A0A3Q0FYN1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087R4Z8_A0A087R4Z8_APTFO_9233 and tr_A0A0A0A237_A0A0A0A237_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087R4Z8_A0A087R4Z8_APTFO_9233 and tr_A0A091HPP2_A0A091HPP2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0G4PEU2_A0A0G4PEU2_PENCA_1429867 and tr_A0A101MRI4_A0A101MRI4_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0G4PEU2_A0A0G4PEU2_PENCA_1429867 and tr_A0A1V6QU85_A0A1V6QU85_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0V1CXE1_A0A0V1CXE1_TRIBR_45882 and tr_A0A0V0WZ11_A0A0V0WZ11_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CXE1_A0A0V1CXE1_TRIBR_45882 and tr_A0A0V0VIE7_A0A0V0VIE7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CXE1_A0A0V1CXE1_TRIBR_45882 and tr_A0A0V1LTE5_A0A0V1LTE5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CXE1_A0A0V1CXE1_TRIBR_45882 and tr_A0A0V1NTC7_A0A0V1NTC7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A2U4A302_A0A2U4A302_TURTR_9739 and tr_A0A2Y9NRU6_A0A2Y9NRU6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A302_A0A2U4A302_TURTR_9739 and tr_A0A2Y9TDD4_A0A2Y9TDD4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZVF8_A0A2U3ZVF8_ODORO_9708 and tr_A0A2U3XPN8_A0A2U3XPN8_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.raxml.reduced.phy Alignment comprises 1 partitions and 478 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 478 Gaps: 46.82 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.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_300621/phylogeny-snakemake/results/Q9UNN4/3_mltree/Q9UNN4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600 [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: -185305.173899 [00:00:00 -185305.173899] Initial branch length optimization [00:00:01 -155219.803356] Model parameter optimization (eps = 0.100000) [00:00:30] Tree #1, final logLikelihood: -154844.861059 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.090011,0.224931) (0.080179,0.284786) (0.153829,0.587758) (0.675981,1.281849) 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_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UNN4/4_raxmlng_ancestral/Q9UNN4.raxml.log Analysis started: 19-Jul-2021 13:45:01 / finished: 19-Jul-2021 13:45:36 Elapsed time: 34.488 seconds