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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 17:53:09 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/2_msa/Q13233_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/3_mltree/Q13233.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/4_raxmlng_ancestral/Q13233 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622645589 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/Q13233/2_msa/Q13233_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 1512 sites WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_A0A2J8UZE7_A0A2J8UZE7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_H2QDN0_H2QDN0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and sp_Q99759_M3K3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_A0A1D5QJ66_A0A1D5QJ66_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_A0A0D9QV48_A0A0D9QV48_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_A0A2K5LLI5_A0A2K5LLI5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S871_G3S871_GORGO_9595 and tr_A0A2K6CXJ8_A0A2K6CXJ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_B8PHX0_B8PHX0_POSPM_561896 and tr_A0A1X6N9B6_A0A1X6N9B6_9APHY_670580 are exactly identical! WARNING: Sequences tr_F1P750_F1P750_CANLF_9615 and tr_A0A2U3WBV8_A0A2U3WBV8_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2QIN7_H2QIN7_PANTR_9598 and tr_A0A2R9B1W3_A0A2R9B1W3_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PV09_W5PV09_SHEEP_9940 and tr_F1MH06_F1MH06_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FRT8_F9FRT8_FUSOF_660025 and tr_A0A0D2XZI2_A0A0D2XZI2_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FRT8_F9FRT8_FUSOF_660025 and tr_A0A2H3TI68_A0A2H3TI68_FUSOX_5507 are exactly identical! WARNING: Sequences tr_J4WHB8_J4WHB8_BEAB2_655819 and tr_A0A0A2VH48_A0A0A2VH48_BEABA_1245745 are exactly identical! WARNING: Sequences sp_Q9Y2U5_M3K2_HUMAN_9606 and tr_U3EYD6_U3EYD6_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q9Y2U5_M3K2_HUMAN_9606 and tr_A0A2K5KPM4_A0A2K5KPM4_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9Y2U5_M3K2_HUMAN_9606 and tr_A0A2K6AJH1_A0A2K6AJH1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0E0IZF4_A0A0E0IZF4_ORYNI_4536 and tr_I1QYH1_I1QYH1_ORYGL_4538 are exactly identical! WARNING: Sequences tr_F6YLW2_F6YLW2_MACMU_9544 and tr_A0A0D9RW94_A0A0D9RW94_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6YLW2_F6YLW2_MACMU_9544 and tr_A0A2K6DC21_A0A2K6DC21_MACNE_9545 are exactly identical! WARNING: Sequences tr_B8BF19_B8BF19_ORYSI_39946 and tr_A0A0E0QQU7_A0A0E0QQU7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8BF19_B8BF19_ORYSI_39946 and tr_A0A0E0B2F4_A0A0E0B2F4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1QNL4_I1QNL4_ORYGL_4538 and tr_A0A0D3H6B3_A0A0D3H6B3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_M7YGI4_M7YGI4_TRIUA_4572 and tr_A0A3B6B3I4_A0A3B6B3I4_WHEAT_4565 are exactly identical! WARNING: Sequences tr_V2XTC6_V2XTC6_MONRO_1381753 and tr_A0A0W0GDQ1_A0A0W0GDQ1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A3B6KFL8_A0A3B6KFL8_WHEAT_4565 and tr_A0A3B6MSP6_A0A3B6MSP6_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067EMC6_A0A067EMC6_CITSI_2711 and tr_V4T553_V4T553_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067G591_A0A067G591_CITSI_2711 and tr_V4S2W2_V4S2W2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067G591_A0A067G591_CITSI_2711 and tr_A0A2H5NQY6_A0A2H5NQY6_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078F5I6_A0A078F5I6_BRANA_3708 and tr_A0A078I395_A0A078I395_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A078F5I6_A0A078F5I6_BRANA_3708 and tr_A0A0D3E4J8_A0A0D3E4J8_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2V143_A0A0D2V143_GOSRA_29730 and tr_A0A1U8PL25_A0A1U8PL25_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1S3XVF7_A0A1S3XVF7_TOBAC_4097 and tr_A0A1U7W807_A0A1U7W807_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4ADQ5_A0A1S4ADQ5_TOBAC_4097 and sp_Q40541_NPK1_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S4D710_A0A1S4D710_TOBAC_4097 and tr_A0A1U7VGC8_A0A1U7VGC8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2H3E1E3_A0A2H3E1E3_ARMGA_47427 and tr_A0A2H3CMX2_A0A2H3CMX2_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2I4GH26_A0A2I4GH26_JUGRE_51240 and tr_A0A2I4GI36_A0A2I4GI36_JUGRE_51240 are exactly identical! WARNING: Sequences tr_A0A2I4GH26_A0A2I4GH26_JUGRE_51240 and tr_A0A2I4GI47_A0A2I4GI47_JUGRE_51240 are exactly identical! WARNING: Sequences tr_A0A2I4GH26_A0A2I4GH26_JUGRE_51240 and tr_A0A2I4HB10_A0A2I4HB10_JUGRE_51240 are exactly identical! WARNING: Sequences tr_A0A384CBN1_A0A384CBN1_URSMA_29073 and tr_A0A383ZL56_A0A383ZL56_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q13233/4_raxmlng_ancestral/Q13233.raxml.reduced.phy Alignment comprises 1 partitions and 1512 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1512 Gaps: 63.05 % Invariant sites: 0.79 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/4_raxmlng_ancestral/Q13233.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/Q13233/3_mltree/Q13233.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 378 / 30240 [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: -360068.534791 [00:00:00 -360068.534791] Initial branch length optimization [00:00:07 -321566.314560] Model parameter optimization (eps = 0.100000) [00:02:55] Tree #1, final logLikelihood: -320607.695452 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.062516,0.140486) (0.070992,0.160515) (0.294058,0.629780) (0.572434,1.388160) 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/Q13233/4_raxmlng_ancestral/Q13233.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/4_raxmlng_ancestral/Q13233.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/4_raxmlng_ancestral/Q13233.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13233/4_raxmlng_ancestral/Q13233.raxml.log Analysis started: 02-Jun-2021 17:53:09 / finished: 02-Jun-2021 17:56:19 Elapsed time: 190.252 seconds Consumed energy: 12.708 Wh