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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 17-Jul-2021 07:34:04 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/2_msa/Q9NVH1_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/3_mltree/Q9NVH1.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626496444 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/2_msa/Q9NVH1_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 559 sites WARNING: Sequences tr_M3Y5V1_M3Y5V1_MUSPF_9669 and tr_A0A2Y9KAV7_A0A2Y9KAV7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3HV79_A0A2I3HV79_NOMLE_61853 and tr_A0A2I2ZKD6_A0A2I2ZKD6_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A087ZY83_A0A087ZY83_APIME_7460 and tr_A0A2A3EF73_A0A2A3EF73_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0G5D4_A0A0E0G5D4_ORYNI_4536 and tr_A0A0D9YR01_A0A0D9YR01_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H4U8_A0A0E0H4U8_ORYNI_4536 and tr_Q337D7_Q337D7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_A2Y7F9_A2Y7F9_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_I1PXX3_I1PXX3_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_A0A0E0PR78_A0A0E0PR78_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_A0A0D3GAS7_A0A0D3GAS7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_A0A0E0A2S3_A0A0E0A2S3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HIE7_A0A0E0HIE7_ORYNI_4536 and tr_Q688X8_Q688X8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H9END8_H9END8_MACMU_9544 and tr_A0A096NF19_A0A096NF19_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9END8_H9END8_MACMU_9544 and tr_A0A0D9S8R7_A0A0D9S8R7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9END8_H9END8_MACMU_9544 and tr_A0A2K5MUE4_A0A2K5MUE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9END8_H9END8_MACMU_9544 and tr_A0A2K6CAQ0_A0A2K6CAQ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_I1NZQ4_I1NZQ4_ORYGL_4538 and tr_A0A0D3F438_A0A0D3F438_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PS46_I1PS46_ORYGL_4538 and tr_A0A0E0PGZ8_A0A0E0PGZ8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1PS46_I1PS46_ORYGL_4538 and tr_A0A0D9ZTQ3_A0A0D9ZTQ3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B3RQK7_B3RQK7_TRIAD_10228 and tr_A0A369S6Q7_A0A369S6Q7_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4CAV8_M4CAV8_BRARP_51351 and tr_A0A078JQX0_A0A078JQX0_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DVG1_M4DVG1_BRARP_51351 and tr_A0A0D3AXM6_A0A0D3AXM6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M4ELR0_M4ELR0_BRARP_51351 and tr_A0A078JEQ8_A0A078JEQ8_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2QTZ8_W2QTZ8_PHYPN_761204 and tr_A0A0W8DZ23_A0A0W8DZ23_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QTZ8_W2QTZ8_PHYPN_761204 and tr_W2K3Y9_W2K3Y9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015JTS4_A0A015JTS4_9GLOM_1432141 and tr_A0A2H5TEV2_A0A2H5TEV2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067GLT6_A0A067GLT6_CITSI_2711 and tr_V4UCP7_V4UCP7_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078G6P4_A0A078G6P4_BRANA_3708 and tr_A0A0D3DNW7_A0A0D3DNW7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078GBV4_A0A078GBV4_BRANA_3708 and tr_A0A0D3AF02_A0A0D3AF02_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078GWN6_A0A078GWN6_BRANA_3708 and tr_A0A0D3E5G4_A0A0D3E5G4_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JI59_A0A078JI59_BRANA_3708 and tr_A0A0D3DWD2_A0A0D3DWD2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4SPQ8_V4SPQ8_9ROSI_85681 and tr_A0A2H5QK75_A0A2H5QK75_CITUN_55188 are exactly identical! WARNING: Sequences tr_V4TSL8_V4TSL8_9ROSI_85681 and tr_A0A2H5NFN4_A0A2H5NFN4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2TR88_A0A0D2TR88_GOSRA_29730 and tr_A0A1U8KL17_A0A1U8KL17_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091JP28_A0A091JP28_EGRGA_188379 and tr_A0A0A0AMF1_A0A0A0AMF1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3Z024_A0A1S3Z024_TOBAC_4097 and tr_A0A1J6K1W4_A0A1J6K1W4_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3Z024_A0A1S3Z024_TOBAC_4097 and tr_A0A1U7WVV8_A0A1U7WVV8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DRC2_A0A1S4DRC2_TOBAC_4097 and tr_A0A1U7VHB2_A0A1U7VHB2_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q6EIX9_Q6EIX9_TOBAC_4097 and tr_A0A1U7YJI3_A0A1U7YJI3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8I0W8_A0A1U8I0W8_GOSHI_3635 and tr_A0A1U8PDE0_A0A1U8PDE0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1U8DSI1_A0A1U8DSI1_CAPAN_4072 and tr_A0A2G3BSK9_A0A2G3BSK9_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 40 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.raxml.reduced.phy Alignment comprises 1 partitions and 559 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 559 Gaps: 37.69 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/3_mltree/Q9NVH1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 140 / 11200 [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: -213258.414650 [00:00:00 -213258.414650] Initial branch length optimization [00:00:01 -212051.661855] Model parameter optimization (eps = 0.100000) [00:00:43] Tree #1, final logLikelihood: -211073.708843 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.107753,0.447168) (0.165217,0.734328) (0.476682,0.943151) (0.250348,1.521520) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NVH1/4_raxmlng_ancestral/Q9NVH1.raxml.log Analysis started: 17-Jul-2021 07:34:04 / finished: 17-Jul-2021 07:34:52 Elapsed time: 48.782 seconds