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 00:29:16 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/2_msa/Q92947_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/3_mltree/Q92947.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/4_raxmlng_ancestral/Q92947 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397356 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/Q92947/2_msa/Q92947_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 438 sites WARNING: Sequences tr_B6QT42_B6QT42_TALMQ_441960 and tr_A0A093VA35_A0A093VA35_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B8P927_B8P927_POSPM_561896 and tr_A0A1X6MZ96_A0A1X6MZ96_9APHY_670580 are exactly identical! WARNING: Sequences tr_Q29PD4_Q29PD4_DROPS_46245 and tr_B4GKJ7_B4GKJ7_DROPE_7234 are exactly identical! WARNING: Sequences tr_K7CAF6_K7CAF6_PANTR_9598 and tr_A0A2R8ZQM3_A0A2R8ZQM3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9G7Y3_F9G7Y3_FUSOF_660025 and tr_N4UVU2_N4UVU2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G7Y3_F9G7Y3_FUSOF_660025 and tr_X0CFP6_X0CFP6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G7Y3_F9G7Y3_FUSOF_660025 and tr_A0A2H3TIJ0_A0A2H3TIJ0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G7Y3_F9G7Y3_FUSOF_660025 and tr_A0A2H3GKI6_A0A2H3GKI6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9EY13_E9EY13_METRA_655844 and tr_A0A0B4HWP4_A0A0B4HWP4_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EY13_E9EY13_METRA_655844 and tr_A0A0D9P502_A0A0D9P502_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HH48_C6HH48_AJECH_544712 and tr_F0URW7_F0URW7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q2U548_Q2U548_ASPOR_510516 and tr_A0A1S9DIS4_A0A1S9DIS4_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2U548_Q2U548_ASPOR_510516 and tr_A0A2G7G9K6_A0A2G7G9K6_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0E0FGK3_A0A0E0FGK3_ORYNI_4536 and tr_I1NKF5_I1NKF5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FGK3_A0A0E0FGK3_ORYNI_4536 and tr_A0A0D3EJV4_A0A0D3EJV4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FGK3_A0A0E0FGK3_ORYNI_4536 and tr_A0A0D9Y3J9_A0A0D9Y3J9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HQK1_A0A0E0HQK1_ORYNI_4536 and tr_A0A0E0PXK5_A0A0E0PXK5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A5ABU5_A5ABU5_ASPNC_425011 and tr_A0A319AJH8_A0A319AJH8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7F1J7_F7F1J7_MACMU_9544 and tr_A0A2K6CHA6_A0A2K6CHA6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XFH4_G7XFH4_ASPKW_1033177 and tr_A0A146FRV5_A0A146FRV5_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XFH4_G7XFH4_ASPKW_1033177 and tr_A0A146FS25_A0A146FS25_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2WKY4_A2WKY4_ORYSI_39946 and tr_A0A0E0MRM6_A0A0E0MRM6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2WKY4_A2WKY4_ORYSI_39946 and tr_Q5ZEL4_Q5ZEL4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1PSR5_I1PSR5_ORYGL_4538 and tr_A0A0E0DMJ1_A0A0E0DMJ1_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1PSR5_I1PSR5_ORYGL_4538 and tr_A0A0D9ZUN0_A0A0D9ZUN0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9XE99_F9XE99_ZYMTI_336722 and tr_A0A1X7RX57_A0A1X7RX57_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_W2RC03_W2RC03_PHYPN_761204 and tr_W2LHH1_W2LHH1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015I5I7_A0A015I5I7_9GLOM_1432141 and tr_A0A2I1G4V2_A0A2I1G4V2_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015I5I7_A0A015I5I7_9GLOM_1432141 and tr_U9U0J5_U9U0J5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094EDV8_A0A094EDV8_9PEZI_1420912 and tr_A0A1B8GVC4_A0A1B8GVC4_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F9ZZF8_A0A0F9ZZF8_TRIHA_5544 and tr_A0A2T4AFV2_A0A2T4AFV2_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0A1NJJ0_A0A0A1NJJ0_9FUNG_58291 and tr_A0A367K5A8_A0A367K5A8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A1S3Y093_A0A1S3Y093_TOBAC_4097 and tr_A0A1U7YDF5_A0A1U7YDF5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1D1W8Q8_A0A1D1W8Q8_RAMVA_947166 and tr_A0A1D1WB38_A0A1D1WB38_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1V8V8P8_A0A1V8V8P8_9PEZI_1974281 and tr_A0A1V8SJY4_A0A1V8SJY4_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1V8V8P8_A0A1V8V8P8_9PEZI_1974281 and tr_A0A1V8TJB4_A0A1V8TJB4_9PEZI_1507870 are exactly identical! WARNING: Duplicate sequences found: 36 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/Q92947/4_raxmlng_ancestral/Q92947.raxml.reduced.phy Alignment comprises 1 partitions and 438 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 438 Gaps: 10.07 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/4_raxmlng_ancestral/Q92947.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/Q92947/3_mltree/Q92947.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 110 / 8800 [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: -166517.133874 [00:00:00 -166517.133874] Initial branch length optimization [00:00:01 -166407.025225] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -165760.030485 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.233430,0.361065) (0.289297,0.474848) (0.256885,0.906646) (0.220389,2.474906) 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/Q92947/4_raxmlng_ancestral/Q92947.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/4_raxmlng_ancestral/Q92947.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/4_raxmlng_ancestral/Q92947.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q92947/4_raxmlng_ancestral/Q92947.raxml.log Analysis started: 23-Jun-2021 00:29:16 / finished: 23-Jun-2021 00:30:00 Elapsed time: 44.353 seconds Consumed energy: 3.622 Wh