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 24-Jul-2021 20:59:10 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/2_msa/A6NI47_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/3_mltree/A6NI47.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/4_raxmlng_ancestral/A6NI47 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627149550 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/A6NI47/2_msa/A6NI47_nogap_msa.fasta [00:00:00] Loaded alignment with 994 taxa and 508 sites WARNING: Sequences tr_F1NLN5_F1NLN5_CHICK_9031 and tr_G1NDL4_G1NDL4_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NLN5_F1NLN5_CHICK_9031 and tr_U3IJ93_U3IJ93_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NLN5_F1NLN5_CHICK_9031 and tr_A0A091VE49_A0A091VE49_NIPNI_128390 are exactly identical! WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_E9Q637_E9Q637_MOUSE_10090 are exactly identical! WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_Q8C646_Q8C646_MOUSE_10090 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_G3R7F9_G3R7F9_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_H2PE99_H2PE99_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_H2QQ51_H2QQ51_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and sp_Q9ULJ7_ANR50_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_F7H1K0_F7H1K0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_F6YYW4_F6YYW4_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_G7P687_G7P687_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A096NYI5_A0A096NYI5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A0D9S0M9_A0A0D9S0M9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A2K5MH73_A0A2K5MH73_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A2K6D9V0_A0A2K6D9V0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A2K5YBY3_A0A2K5YBY3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RE75_G1RE75_NOMLE_61853 and tr_A0A2R9CD42_A0A2R9CD42_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8NQZ3_B8NQZ3_ASPFN_332952 and tr_A0A1S9DSF0_A0A1S9DSF0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_E2RR81_E2RR81_CANLF_9615 and tr_A0A2U3X075_A0A2U3X075_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and sp_Q92527_ANKR7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and tr_A0A2R8ZJB4_A0A2R8ZJB4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7CR95_F7CR95_MONDO_13616 and tr_G3VYV3_G3VYV3_SARHA_9305 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_G3TDW7_G3TDW7_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_I3LD98_I3LD98_PIG_9823 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_E1B7G6_E1B7G6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A2U4AR74_A0A2U4AR74_TURTR_9739 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A2Y9E5S2_A0A2Y9E5S2_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A2Y9KE62_A0A2Y9KE62_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A2Y9Q3C9_A0A2Y9Q3C9_DELLE_9749 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A2Y9F066_A0A2Y9F066_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H0VMD2_H0VMD2_CAVPO_10141 and tr_A0A383ZBC3_A0A383ZBC3_BALAS_310752 are exactly identical! WARNING: Sequences sp_A0A0A6YYL3_POTEB_HUMAN_9606 and sp_H3BUK9_POTB2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5SQ80_A20A2_HUMAN_9606 and sp_Q5VUR7_A20A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q2UGY0_Q2UGY0_ASPOR_510516 and tr_A0A1S9DZ77_A0A1S9DZ77_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A091EUN4_A0A091EUN4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A093QHA6_A0A093QHA6_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A218UXQ1_A0A218UXQ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096MVX0_A0A096MVX0_PAPAN_9555 and tr_A0A2K5KKK9_A0A2K5KKK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0Q3PN20_A0A0Q3PN20_AMAAE_12930 and tr_A0A099ZVA7_A0A099ZVA7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0Q3PN20_A0A0Q3PN20_AMAAE_12930 and tr_A0A093IB22_A0A093IB22_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VSL6_A0A091VSL6_OPIHO_30419 and tr_A0A2I0MGU1_A0A2I0MGU1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091VSL6_A0A091VSL6_OPIHO_30419 and tr_A0A091IHK1_A0A091IHK1_CALAN_9244 are exactly identical! WARNING: Duplicate sequences found: 43 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/A6NI47/4_raxmlng_ancestral/A6NI47.raxml.reduced.phy Alignment comprises 1 partitions and 508 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 508 Gaps: 47.71 % Invariant sites: 0.00 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/4_raxmlng_ancestral/A6NI47.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/A6NI47/3_mltree/A6NI47.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 127 / 10160 [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: -303151.089285 [00:00:00 -303151.089285] Initial branch length optimization [00:00:02 -275546.259620] Model parameter optimization (eps = 0.100000) [00:00:18] Tree #1, final logLikelihood: -275407.032812 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.053249,0.092513) (0.097327,0.322049) (0.433023,0.675506) (0.416400,1.611957) 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/A6NI47/4_raxmlng_ancestral/A6NI47.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/4_raxmlng_ancestral/A6NI47.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/4_raxmlng_ancestral/A6NI47.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NI47/4_raxmlng_ancestral/A6NI47.raxml.log Analysis started: 24-Jul-2021 20:59:10 / finished: 24-Jul-2021 20:59:33 Elapsed time: 23.114 seconds