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 17:56:10 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/2_msa/Q96D31_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/4_raxmlng_ancestral/Q96D31 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101770 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/Q96D31/2_msa/Q96D31_nogap_msa.fasta [00:00:00] Loaded alignment with 427 taxa and 301 sites WARNING: Sequences tr_B4QBS3_B4QBS3_DROSI_7240 and tr_B4HN91_B4HN91_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A226NB30_A0A226NB30_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A226PGN0_A0A226PGN0_COLVI_9014 are exactly identical! WARNING: Sequences tr_G3RIY1_G3RIY1_GORGO_9595 and sp_Q96SN7_ORAI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_H2NQQ8_H2NQQ8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_K7B6T1_K7B6T1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8XU32_A0A2J8XU32_PONAB_9601 and tr_G7P152_G7P152_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8XU32_A0A2J8XU32_PONAB_9601 and tr_A0A2K6AMG3_A0A2K6AMG3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8XU32_A0A2J8XU32_PONAB_9601 and tr_A0A2K5XH72_A0A2K5XH72_MANLE_9568 are exactly identical! WARNING: Sequences tr_N6W572_N6W572_DROPS_46245 and tr_B4GIU1_B4GIU1_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3SMW8_A0A2I3SMW8_PANTR_9598 and tr_A0A2R9BE06_A0A2R9BE06_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NR30_A0A158NR30_ATTCE_12957 and tr_A0A151HYU7_A0A151HYU7_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5RK59_A0A1D5RK59_MACMU_9544 and tr_A0A2K6CAQ5_A0A2K6CAQ5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GY76_F7GY76_MACMU_9544 and tr_A0A2I3LPN3_A0A2I3LPN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GY76_F7GY76_MACMU_9544 and tr_A0A0D9RZQ9_A0A0D9RZQ9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A151XB59_A0A151XB59_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A195DI95_A0A195DI95_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A195BD97_A0A195BD97_9HYME_520822 are exactly identical! WARNING: Sequences sp_Q616J1_ORAI_CAEBR_6238 and tr_A0A2G5UME7_A0A2G5UME7_9PELO_1611254 are exactly identical! WARNING: Sequences tr_U3K4E8_U3K4E8_FICAL_59894 and tr_A0A091F6Q1_A0A091F6Q1_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3K4E8_U3K4E8_FICAL_59894 and tr_A0A093QJ02_A0A093QJ02_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3K4E8_U3K4E8_FICAL_59894 and tr_A0A087QHV0_A0A087QHV0_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3K4E8_U3K4E8_FICAL_59894 and tr_A0A218V1R2_A0A218V1R2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A044VCV3_A0A044VCV3_ONCVO_6282 and tr_A0A182EE33_A0A182EE33_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D9R0H3_A0A0D9R0H3_CHLSB_60711 and tr_A0A2K5MQE4_A0A2K5MQE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R0H3_A0A0D9R0H3_CHLSB_60711 and tr_A0A2K5Z8S0_A0A2K5Z8S0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NSH5_A0A151NSH5_ALLMI_8496 and tr_A0A1U7RJ36_A0A1U7RJ36_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0N0BC83_A0A0N0BC83_9HYME_166423 and tr_A0A0L7R8M8_A0A0L7R8M8_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A2I0M8L0_A0A2I0M8L0_COLLI_8932 and tr_A0A1V4JSA0_A0A1V4JSA0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V0ZNY3_A0A0V0ZNY3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 and tr_A0A0V0WME7_A0A0V0WME7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 and tr_A0A0V0VIN1_A0A0V0VIN1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 and tr_A0A0V1LPV8_A0A0V1LPV8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 and tr_A0A0V1P396_A0A0V1P396_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 and tr_A0A0V0TUI4_A0A0V0TUI4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0YEF6_A0A0V0YEF6_TRIPS_6337 and tr_A0A0V1I901_A0A0V1I901_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3PHW9_A0A1S3PHW9_SALSA_8030 and tr_A0A060WEB6_A0A060WEB6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226N985_A0A226N985_CALSU_9009 and tr_A0A226PZ61_A0A226PZ61_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3VQ40_A0A2U3VQ40_ODORO_9708 and tr_A0A2U3XEM0_A0A2U3XEM0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9PL09_A0A2Y9PL09_DELLE_9749 and tr_A0A384AGL9_A0A384AGL9_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q96D31/4_raxmlng_ancestral/Q96D31.raxml.reduced.phy Alignment comprises 1 partitions and 301 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 301 Gaps: 25.15 % Invariant sites: 0.33 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/4_raxmlng_ancestral/Q96D31.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/Q96D31/3_mltree/Q96D31.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 76 / 6080 [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: -52350.027675 [00:00:00 -52350.027675] Initial branch length optimization [00:00:00 -39273.792318] Model parameter optimization (eps = 0.100000) [00:00:28] Tree #1, final logLikelihood: -38886.937299 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.226211,0.096478) (0.244285,0.157888) (0.284987,0.642986) (0.244516,3.093307) 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/Q96D31/4_raxmlng_ancestral/Q96D31.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/4_raxmlng_ancestral/Q96D31.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/4_raxmlng_ancestral/Q96D31.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/4_raxmlng_ancestral/Q96D31.raxml.log Analysis started: 12-Jul-2021 17:56:10 / finished: 12-Jul-2021 17:56:39 Elapsed time: 29.508 seconds Consumed energy: 2.464 Wh