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 02:39:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/2_msa/P04839_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/3_mltree/P04839.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/4_raxmlng_ancestral/P04839 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677167 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/P04839/2_msa/P04839_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 570 sites WARNING: Sequences tr_J3K135_J3K135_COCIM_246410 and tr_E9D3D0_E9D3D0_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K135_J3K135_COCIM_246410 and tr_A0A0J6YRM5_A0A0J6YRM5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QAC6_B6QAC6_TALMQ_441960 and tr_A0A093UX21_A0A093UX21_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W585_B2W585_PYRTR_426418 and tr_A0A2W1GC03_A0A2W1GC03_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QXY3_G3QXY3_GORGO_9595 and tr_H2R4R9_H2R4R9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QXY3_G3QXY3_GORGO_9595 and sp_P04839_CY24B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QXY3_G3QXY3_GORGO_9595 and tr_A0A2R9A4U4_A0A2R9A4U4_PANPA_9597 are exactly identical! WARNING: Sequences tr_C0NHF1_C0NHF1_AJECG_447093 and tr_C6H6H3_C6H6H3_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NHF1_C0NHF1_AJECG_447093 and tr_F0UV23_F0UV23_AJEC8_544711 are exactly identical! WARNING: Sequences tr_V5IKM9_V5IKM9_NEUCR_367110 and tr_G4UYG7_G4UYG7_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A179US97_A0A179US97_BLAGS_559298 and tr_C5GPI0_C5GPI0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3RE96_A0A2I3RE96_PANTR_9598 and tr_A0A2R8ZMV9_A0A2R8ZMV9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9F1V9_F9F1V9_FUSOF_660025 and tr_N4TVD6_N4TVD6_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9F1V9_F9F1V9_FUSOF_660025 and tr_X0CQ92_X0CQ92_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9F1V9_F9F1V9_FUSOF_660025 and tr_A0A2H3SRJ3_A0A2H3SRJ3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G7Y5_F9G7Y5_FUSOF_660025 and tr_N4UAN0_N4UAN0_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G7Y5_F9G7Y5_FUSOF_660025 and tr_A0A2H3TUM5_A0A2H3TUM5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G7Y5_F9G7Y5_FUSOF_660025 and tr_A0A2H3GTL6_A0A2H3GTL6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9ELW0_E9ELW0_METRA_655844 and tr_A0A0D9P457_A0A0D9P457_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9EY15_E9EY15_METRA_655844 and tr_A0A0D9P4L8_A0A0D9P4L8_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HQK6_C6HQK6_AJECH_544712 and tr_F0UQ77_F0UQ77_AJEC8_544711 are exactly identical! WARNING: Sequences tr_F6TZ83_F6TZ83_MACMU_9544 and tr_G7PNF0_G7PNF0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X7S5_F6X7S5_MACMU_9544 and tr_G7Q2H9_G7Q2H9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X7S5_F6X7S5_MACMU_9544 and tr_A0A096MRV2_A0A096MRV2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6X7S5_F6X7S5_MACMU_9544 and tr_A0A2K6B439_A0A2K6B439_MACNE_9545 are exactly identical! WARNING: Sequences tr_F9WYZ9_F9WYZ9_ZYMTI_336722 and tr_A0A1X7RE92_A0A1X7RE92_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YNY8_G2YNY8_BOTF4_999810 and tr_M7TSN8_M7TSN8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_C9SQD8_C9SQD8_VERA1_526221 and tr_A0A0G4N268_A0A0G4N268_9PEZI_100787 are exactly identical! WARNING: Sequences tr_W7L9X2_W7L9X2_GIBM7_334819 and tr_S0DNB8_S0DNB8_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7L9X2_W7L9X2_GIBM7_334819 and tr_A0A365MUV9_A0A365MUV9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M4EK77_M4EK77_BRARP_51351 and tr_A0A078H5B7_A0A078H5B7_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4EK77_M4EK77_BRARP_51351 and tr_A0A078HK01_A0A078HK01_BRANA_3708 are exactly identical! WARNING: Sequences tr_S0E9E9_S0E9E9_GIBF5_1279085 and tr_A0A365NQ09_A0A365NQ09_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M2SRS5_M2SRS5_COCSN_665912 and tr_W6XT90_W6XT90_COCCA_930089 are exactly identical! WARNING: Sequences tr_A0A010SDJ4_A0A010SDJ4_9PEZI_1445577 and tr_A0A135T0E4_A0A135T0E4_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A015L2K9_A0A015L2K9_9GLOM_1432141 and tr_A0A2H5RIB9_A0A2H5RIB9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015MWV5_A0A015MWV5_9GLOM_1432141 and tr_U9SQZ8_U9SQZ8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0F0ICD7_A0A0F0ICD7_ASPPU_1403190 and tr_A0A2G7FKI4_A0A2G7FKI4_9EURO_656916 are exactly identical! WARNING: Sequences tr_W6YC62_W6YC62_COCCA_930089 and tr_W6YTL9_W6YTL9_COCMI_930090 are exactly identical! WARNING: Sequences tr_I1RB34_I1RB34_GIBZE_229533 and tr_A0A2T4H6E4_A0A2T4H6E4_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1B8AP84_A0A1B8AP84_FUSPO_36050 and tr_A0A2L2TNU3_A0A2L2TNU3_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A2H3AYU6_A0A2H3AYU6_9AGAR_1076256 and tr_A0A284RPH4_A0A284RPH4_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2K5LNP4_A0A2K5LNP4_CERAT_9531 and tr_A0A2K5ZEB7_A0A2K5ZEB7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2V5I5E5_A0A2V5I5E5_9EURO_1450541 and tr_A0A2V5HAL7_A0A2V5HAL7_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 44 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/P04839/4_raxmlng_ancestral/P04839.raxml.reduced.phy Alignment comprises 1 partitions and 570 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 570 Gaps: 11.63 % Invariant sites: 1.23 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/4_raxmlng_ancestral/P04839.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/P04839/3_mltree/P04839.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440 [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: -198876.596430 [00:00:00 -198876.596430] Initial branch length optimization [00:00:01 -198353.341815] Model parameter optimization (eps = 0.100000) [00:00:33] Tree #1, final logLikelihood: -197885.205344 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.201053,0.350794) (0.297312,0.537917) (0.349816,1.153507) (0.151819,2.410948) 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/P04839/4_raxmlng_ancestral/P04839.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/4_raxmlng_ancestral/P04839.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/4_raxmlng_ancestral/P04839.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04839/4_raxmlng_ancestral/P04839.raxml.log Analysis started: 03-Jun-2021 02:39:27 / finished: 03-Jun-2021 02:40:06 Elapsed time: 38.479 seconds Consumed energy: 3.036 Wh