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 23-Jun-2021 00:30:20 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/2_msa/Q695T7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/3_mltree/Q695T7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397420 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/030621_run/phylogeny-snakemake/results/Q695T7/2_msa/Q695T7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 634 sites WARNING: Sequences tr_B4QCY5_B4QCY5_DROSI_7240 and tr_B4HNQ4_B4HNQ4_DROSE_7238 are exactly identical! WARNING: Sequences sp_P31648_SC6A1_MOUSE_10090 and sp_P23978_SC6A1_RAT_10116 are exactly identical! WARNING: Sequences tr_G1QZV9_G1QZV9_NOMLE_61853 and sp_Q9H2J7_S6A15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QZV9_G1QZV9_NOMLE_61853 and tr_A0A2R9CFW0_A0A2R9CFW0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2PA22_H2PA22_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2QM23_H2QM23_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and sp_P30531_SC6A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6WVM8_F6WVM8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_G7NYT4_G7NYT4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A096NQ20_A0A096NQ20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A0D9RC09_A0A0D9RC09_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6A0C9_A0A2K6A0C9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2R9CH47_A0A2R9CH47_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F7F7H9_F7F7H9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_G7PQK0_G7PQK0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A096NG10_A0A096NG10_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A0D9QYL3_A0A0D9QYL3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K5MCU9_A0A2K5MCU9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K6ECY9_A0A2K6ECY9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K5YI07_A0A2K5YI07_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RBF7_G3RBF7_GORGO_9595 and tr_A0A2I3SQC1_A0A2I3SQC1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RBF7_G3RBF7_GORGO_9595 and sp_Q9H1V8_S6A17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RBF7_G3RBF7_GORGO_9595 and tr_A0A2R9CBH2_A0A2R9CBH2_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RKV9_E2RKV9_CANLF_9615 and tr_A0A2I2UPJ1_A0A2I2UPJ1_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RKV9_E2RKV9_CANLF_9615 and tr_A0A2U3YMF9_A0A2U3YMF9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3TVI5_A0A2I3TVI5_PANTR_9598 and tr_A0A2R9AZP0_A0A2R9AZP0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and sp_Q9Y345_SC6A5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and tr_A0A2R9AHV1_A0A2R9AHV1_PANPA_9597 are exactly identical! WARNING: Sequences sp_P58295_SC6A5_RAT_10116 and tr_A0A1U8CFY0_A0A1U8CFY0_MESAU_10036 are exactly identical! WARNING: Sequences tr_F7GI73_F7GI73_MACMU_9544 and tr_A0A2K6APZ3_A0A2K6APZ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MIF5_G7MIF5_MACMU_9544 and tr_A0A2K5P0F8_A0A2K5P0F8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MIF5_G7MIF5_MACMU_9544 and tr_A0A2K6CT60_A0A2K6CT60_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0YRJ3_H0YRJ3_TAEGU_59729 and tr_A0A218USV0_A0A218USV0_9PASE_299123 are exactly identical! WARNING: Sequences tr_B3S9D7_B3S9D7_TRIAD_10228 and tr_A0A369RRI9_A0A369RRI9_9METZ_287889 are exactly identical! WARNING: Sequences tr_U3JB51_U3JB51_FICAL_59894 and tr_A0A218UPJ2_A0A218UPJ2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A151NIH4_A0A151NIH4_ALLMI_8496 and tr_A0A1U7SBY4_A0A1U7SBY4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A087RH38_A0A087RH38_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A0A0ATB2_A0A0A0ATB2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093I2B1_A0A093I2B1_STRCA_441894 and tr_A0A226P2N5_A0A226P2N5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1V4JPB2_A0A1V4JPB2_PATFA_372326 and tr_A0A226MWW0_A0A226MWW0_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A226NNI9_A0A226NNI9_CALSU_9009 and tr_A0A226P192_A0A226P192_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QF35_A0A2D0QF35_ICTPU_7998 and tr_A0A2D0QGM6_A0A2D0QGM6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KZH8_A0A2K5KZH8_CERAT_9531 and tr_A0A2K6BVQ8_A0A2K6BVQ8_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 43 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.raxml.reduced.phy Alignment comprises 1 partitions and 634 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 634 Gaps: 10.57 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.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/030621_run/phylogeny-snakemake/results/Q695T7/3_mltree/Q695T7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 159 / 12720 [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: -237058.926417 [00:00:00 -237058.926417] Initial branch length optimization [00:00:01 -232774.846307] Model parameter optimization (eps = 0.100000) [00:00:36] Tree #1, final logLikelihood: -231983.855823 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.229726,0.333103) (0.290401,0.441434) (0.301363,1.158277) (0.178510,2.499711) 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/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q695T7/4_raxmlng_ancestral/Q695T7.raxml.log Analysis started: 23-Jun-2021 00:30:20 / finished: 23-Jun-2021 00:31:01 Elapsed time: 41.894 seconds Consumed energy: 3.319 Wh