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 17:42:50 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/2_msa/O00459_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/3_mltree/O00459.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/4_raxmlng_ancestral/O00459 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100970 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/O00459/2_msa/O00459_nogap_msa.fasta [00:00:00] Loaded alignment with 953 taxa and 728 sites WARNING: Sequences tr_B4Q624_B4Q624_DROSI_7240 and tr_B4ICV4_B4ICV4_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q8AYA6_Q8AYA6_CHICK_9031 and tr_A0A226MNK9_A0A226MNK9_CALSU_9009 are exactly identical! WARNING: Sequences tr_M3YTF0_M3YTF0_MUSPF_9669 and tr_A0A2Y9KPA9_A0A2Y9KPA9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3RH39_A0A2I3RH39_PANTR_9598 and tr_A0A2R8ZHS7_A0A2R8ZHS7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QEP3_H2QEP3_PANTR_9598 and tr_A0A2R9AWS5_A0A2R9AWS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and sp_P42685_FRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and tr_A0A2R9BRU0_A0A2R9BRU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZTP6_A0A087ZTP6_APIME_7460 and tr_A0A2A3ENF5_A0A2A3ENF5_APICC_94128 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2K6BD32_A0A2K6BD32_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BD31_F7BD31_MACMU_9544 and tr_A0A2K5Y133_A0A2K5Y133_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BZL6_F7BZL6_MACMU_9544 and tr_A0A096MNU6_A0A096MNU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BZL6_F7BZL6_MACMU_9544 and tr_A0A2K6D4C7_A0A2K6D4C7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BZL6_F7BZL6_MACMU_9544 and tr_A0A2K6A179_A0A2K6A179_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9ERN5_H9ERN5_MACMU_9544 and tr_A0A2I3MDT8_A0A2I3MDT8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9ERN5_H9ERN5_MACMU_9544 and tr_A0A2K6B3R8_A0A2K6B3R8_MACNE_9545 are exactly identical! WARNING: Sequences tr_D2H2X3_D2H2X3_AILME_9646 and tr_A0A384BPR1_A0A384BPR1_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A0D9S7F0_A0A0D9S7F0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2K5MQ86_A0A2K5MQ86_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2K5ZT21_A0A2K5ZT21_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2U3XCA0_A0A2U3XCA0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A384CRN7_A0A384CRN7_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A151NF33_A0A151NF33_ALLMI_8496 and tr_A0A1U7S2A6_A0A1U7S2A6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VZH1_A0A091VZH1_NIPNI_128390 and tr_A0A0A0AIH7_A0A0A0AIH7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A087RBY7_A0A087RBY7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A091XQ08_A0A091XQ08_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A091GMV4_A0A091GMV4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0V1CM40_A0A0V1CM40_TRIBR_45882 and tr_A0A0V0WYN8_A0A0V0WYN8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CM40_A0A0V1CM40_TRIBR_45882 and tr_A0A0V1A0A4_A0A0V1A0A4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1D3K6_A0A0V1D3K6_TRIBR_45882 and tr_A0A0V1PI33_A0A0V1PI33_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L3L3_A0A0V1L3L3_9BILA_6335 and tr_A0A0V1PCK5_A0A0V1PCK5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L3L3_A0A0V1L3L3_9BILA_6335 and tr_A0A0V0TV42_A0A0V0TV42_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226NKM7_A0A226NKM7_CALSU_9009 and tr_A0A226NQZ1_A0A226NQZ1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4AMH0_A0A2U4AMH0_TURTR_9739 and tr_A0A2Y9NYU8_A0A2Y9NYU8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BI55_A0A2U4BI55_TURTR_9739 and tr_A0A2Y9TFL9_A0A2Y9TFL9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BI55_A0A2U4BI55_TURTR_9739 and tr_A0A384ASB4_A0A384ASB4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BK23_A0A2U4BK23_TURTR_9739 and tr_A0A2Y9NAQ0_A0A2Y9NAQ0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BK23_A0A2U4BK23_TURTR_9739 and tr_A0A383YPD9_A0A383YPD9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9NBA6_A0A2Y9NBA6_DELLE_9749 and tr_A0A383Z0R7_A0A383Z0R7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9S9X6_A0A2Y9S9X6_PHYCD_9755 and tr_A0A383Z3A4_A0A383Z3A4_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 39 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/O00459/4_raxmlng_ancestral/O00459.raxml.reduced.phy Alignment comprises 1 partitions and 728 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 728 Gaps: 43.36 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/4_raxmlng_ancestral/O00459.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/O00459/3_mltree/O00459.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 182 / 14560 [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: -188083.628940 [00:00:00 -188083.628940] Initial branch length optimization [00:00:02 -186877.192641] Model parameter optimization (eps = 0.100000) [00:01:09] Tree #1, final logLikelihood: -185940.165907 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.126713,0.424574) (0.068951,0.912862) (0.408698,0.722039) (0.395638,1.486617) 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/O00459/4_raxmlng_ancestral/O00459.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/4_raxmlng_ancestral/O00459.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/4_raxmlng_ancestral/O00459.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00459/4_raxmlng_ancestral/O00459.raxml.log Analysis started: 12-Jul-2021 17:42:50 / finished: 12-Jul-2021 17:44:06 Elapsed time: 76.063 seconds Consumed energy: 6.713 Wh