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 02:39:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/2_msa/P61764_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/3_mltree/P61764.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/4_raxmlng_ancestral/P61764 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677164 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/P61764/2_msa/P61764_nogap_msa.fasta [00:00:00] Loaded alignment with 670 taxa and 594 sites WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and sp_Q5R6D2_STXB1_PONAB_9601 are exactly identical! WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and sp_P61765_STXB1_RAT_10116 are exactly identical! WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and sp_P61764_STXB1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and sp_P61763_STXB1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and tr_A0A0D9RMR5_A0A0D9RMR5_CHLSB_60711 are exactly identical! WARNING: Sequences sp_O08599_STXB1_MOUSE_10090 and tr_A0A1S3FKB7_A0A1S3FKB7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YQV6_M3YQV6_MUSPF_9669 and tr_A0A2U3YVF2_A0A2U3YVF2_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q07327_ROP_DROME_7227 and tr_B4HU03_B4HU03_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QWA1_G3QWA1_GORGO_9595 and tr_H2PZJ4_H2PZJ4_PANTR_9598 are exactly identical! WARNING: Sequences tr_F1P7D2_F1P7D2_CANLF_9615 and tr_G8F4M5_G8F4M5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3RHR4_A0A2I3RHR4_PANTR_9598 and tr_A0A2R9BJQ8_A0A2R9BJQ8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TBU2_A0A2I3TBU2_PANTR_9598 and tr_A0A1D5Q217_A0A1D5Q217_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3TBU2_A0A2I3TBU2_PANTR_9598 and tr_A0A096P203_A0A096P203_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3TBU2_A0A2I3TBU2_PANTR_9598 and tr_A0A2K5NXR8_A0A2K5NXR8_CERAT_9531 are exactly identical! WARNING: Sequences tr_E5S811_E5S811_TRISP_6334 and tr_A0A0V0SEI4_A0A0V0SEI4_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5S811_E5S811_TRISP_6334 and tr_A0A0V1D9G5_A0A0V1D9G5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5S811_E5S811_TRISP_6334 and tr_A0A0V1PH03_A0A0V1PH03_9BILA_92180 are exactly identical! WARNING: Sequences tr_H1A0C1_H1A0C1_TAEGU_59729 and tr_A0A099YR22_A0A099YR22_TINGU_94827 are exactly identical! WARNING: Sequences tr_H1A0C1_H1A0C1_TAEGU_59729 and tr_A0A091IA09_A0A091IA09_CALAN_9244 are exactly identical! WARNING: Sequences tr_E3LCL2_E3LCL2_CAERE_31234 and tr_A0A261CNW9_A0A261CNW9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8XPR8_A8XPR8_CAEBR_6238 and tr_A0A2G5SWD6_A0A2G5SWD6_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A0A091EXV5_A0A091EXV5_CORBR_85066 and tr_A0A091UJ46_A0A091UJ46_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EXV5_A0A091EXV5_CORBR_85066 and tr_A0A087R7Q6_A0A087R7Q6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EXV5_A0A091EXV5_CORBR_85066 and tr_A0A091IC56_A0A091IC56_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091F2D6_A0A091F2D6_CORBR_85066 and tr_A0A091J080_A0A091J080_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F2D6_A0A091F2D6_CORBR_85066 and tr_A0A091ULH9_A0A091ULH9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F2D6_A0A091F2D6_CORBR_85066 and tr_A0A0A0ADS2_A0A0A0ADS2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0X1A8_A0A0V0X1A8_9BILA_92179 and tr_A0A0V0ZZK1_A0A0V0ZZK1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0XQ11_A0A0V0XQ11_TRIPS_6337 and tr_A0A0V1HQZ5_A0A0V1HQZ5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A164W1B5_A0A164W1B5_9HOMO_1314777 and tr_A0A166CR02_A0A166CR02_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3QCA5_A0A1S3QCA5_SALSA_8030 and tr_A0A061AFI4_A0A061AFI4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226NG65_A0A226NG65_CALSU_9009 and tr_A0A226PL38_A0A226PL38_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3BZR8_A0A2H3BZR8_9AGAR_1076256 and tr_A0A284R5A5_A0A284R5A5_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0PU42_A0A2D0PU42_ICTPU_7998 and tr_A0A2D0PY68_A0A2D0PY68_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5P5V8_A0A2K5P5V8_CERAT_9531 and tr_A0A2K6CG34_A0A2K6CG34_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K6DRT5_A0A2K6DRT5_MACNE_9545 and tr_A0A2K6A052_A0A2K6A052_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3VDU0_A0A2U3VDU0_ODORO_9708 and tr_A0A2Y9JBR3_A0A2Y9JBR3_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 37 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/P61764/4_raxmlng_ancestral/P61764.raxml.reduced.phy Alignment comprises 1 partitions and 594 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 594 Gaps: 16.05 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/4_raxmlng_ancestral/P61764.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/P61764/3_mltree/P61764.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 149 / 11920 [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: -169025.870535 [00:00:00 -169025.870535] Initial branch length optimization [00:00:00 -168657.518872] Model parameter optimization (eps = 0.100000) [00:00:58] Tree #1, final logLikelihood: -167994.603097 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.209528,0.504741) (0.211004,0.567058) (0.307132,0.849326) (0.272336,1.886404) 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/P61764/4_raxmlng_ancestral/P61764.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/4_raxmlng_ancestral/P61764.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/4_raxmlng_ancestral/P61764.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P61764/4_raxmlng_ancestral/P61764.raxml.log Analysis started: 03-Jun-2021 02:39:24 / finished: 03-Jun-2021 02:40:27 Elapsed time: 62.786 seconds Consumed energy: 5.552 Wh