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 03-Jun-2021 01:22:19 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/2_msa/Q96QP1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/3_mltree/Q96QP1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622672539 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/020621_run/phylogeny-snakemake/results/Q96QP1/2_msa/Q96QP1_nogap_msa.fasta [00:00:00] Loaded alignment with 420 taxa and 1244 sites WARNING: Sequences tr_G3RGY7_G3RGY7_GORGO_9595 and sp_O00418_EF2K_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B8P0S6_B8P0S6_POSPM_561896 and tr_A0A1X6N6Y9_A0A1X6N6Y9_9APHY_670580 are exactly identical! WARNING: Sequences tr_F9FYX1_F9FYX1_FUSOF_660025 and tr_N4TY41_N4TY41_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F7F8P2_F7F8P2_MACMU_9544 and tr_G7Q0P5_G7Q0P5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A0D2XJM9_A0A0D2XJM9_FUSO4_426428 and tr_N4TI89_N4TI89_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2XJM9_A0A0D2XJM9_FUSO4_426428 and tr_X0CBG3_X0CBG3_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W2Q3B1_W2Q3B1_PHYPN_761204 and tr_W2IU98_W2IU98_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QBD6_W2QBD6_PHYPN_761204 and tr_W2NGJ3_W2NGJ3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015IH54_A0A015IH54_9GLOM_1432141 and tr_A0A2H5TXI4_A0A2H5TXI4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015IPL6_A0A015IPL6_9GLOM_1432141 and tr_A0A2H5SKR4_A0A2H5SKR4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015IWR6_A0A015IWR6_9GLOM_1432141 and tr_A0A2H5SFM1_A0A2H5SFM1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JZ49_A0A015JZ49_9GLOM_1432141 and tr_U9SY09_U9SY09_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015K4H9_A0A015K4H9_9GLOM_1432141 and tr_U9U5G8_U9U5G8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015KCD8_A0A015KCD8_9GLOM_1432141 and tr_A0A2H5TJZ8_A0A2H5TJZ8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015L530_A0A015L530_9GLOM_1432141 and tr_A0A2H5RL99_A0A2H5RL99_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015LQ20_A0A015LQ20_9GLOM_1432141 and tr_A0A2H5UEJ1_A0A2H5UEJ1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015M4B0_A0A015M4B0_9GLOM_1432141 and tr_A0A2H5U4Q0_A0A2H5U4Q0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015MKM2_A0A015MKM2_9GLOM_1432141 and tr_A0A2H5RHM1_A0A2H5RHM1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015N6K5_A0A015N6K5_9GLOM_1432141 and tr_U9TBQ6_U9TBQ6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044TWW7_A0A044TWW7_ONCVO_6282 and tr_A0A182E4P7_A0A182E4P7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NHB9_A0A096NHB9_PAPAN_9555 and tr_A0A0D9R3Y5_A0A0D9R3Y5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NHB9_A0A096NHB9_PAPAN_9555 and tr_A0A2K5LT66_A0A2K5LT66_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0V1D275_A0A0V1D275_TRIBR_45882 and tr_A0A0V0W827_A0A0V0W827_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D275_A0A0V1D275_TRIBR_45882 and tr_A0A0V0VJP8_A0A0V0VJP8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D275_A0A0V1D275_TRIBR_45882 and tr_A0A0V1KSF4_A0A0V1KSF4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D275_A0A0V1D275_TRIBR_45882 and tr_A0A0V1P7N1_A0A0V1P7N1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D275_A0A0V1D275_TRIBR_45882 and tr_A0A0V0TB67_A0A0V0TB67_9BILA_144512 are exactly identical! WARNING: Duplicate sequences found: 27 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.raxml.reduced.phy Alignment comprises 1 partitions and 1244 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1244 Gaps: 58.93 % Invariant sites: 0.24 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.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/020621_run/phylogeny-snakemake/results/Q96QP1/3_mltree/Q96QP1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 311 / 24880 [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: -199352.788874 [00:00:00 -199352.788874] Initial branch length optimization [00:00:00 -180187.473718] Model parameter optimization (eps = 0.100000) [00:00:50] Tree #1, final logLikelihood: -179496.456225 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.097270,0.293711) (0.071529,0.290856) (0.334702,0.631373) (0.496499,1.489036) 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/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96QP1/4_raxmlng_ancestral/Q96QP1.raxml.log Analysis started: 03-Jun-2021 01:22:19 / finished: 03-Jun-2021 01:23:15 Elapsed time: 55.515 seconds Consumed energy: 4.606 Wh