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 14-Jul-2021 23:10:12 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/2_msa/Q9GZR5_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/4_raxmlng_ancestral/Q9GZR5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626293412 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/Q9GZR5/2_msa/Q9GZR5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 314 sites WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_Q9VCZ0_Q9VCZ0_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_B4HEA8_B4HEA8_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_A0A1W4VRB8_A0A1W4VRB8_DROFC_30025 are exactly identical! WARNING: Sequences tr_Q9VCY6_Q9VCY6_DROME_7227 and tr_B4HEP7_B4HEP7_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QWW6_G3QWW6_GORGO_9595 and tr_A0A2R9BFK1_A0A2R9BFK1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2I3T7B5_A0A2I3T7B5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and sp_Q9NYP7_ELOV5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_G7P2V6_G7P2V6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A096NJ95_A0A096NJ95_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A0D9RL39_A0A0D9RL39_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K5NGQ5_A0A2K5NGQ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K6E3N5_A0A2K6E3N5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K6A232_A0A2K6A232_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2R9BBN2_A0A2R9BBN2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PHX6_H2PHX6_PONAB_9601 and sp_Q9NXB9_ELOV2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B5DPB4_B5DPB4_DROPS_46245 and tr_B4GRK8_B4GRK8_DROPE_7234 are exactly identical! WARNING: Sequences tr_B5DYD8_B5DYD8_DROPS_46245 and tr_B4GP39_B4GP39_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q295G9_Q295G9_DROPS_46245 and tr_B4GDX0_B4GDX0_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29BK2_Q29BK2_DROPS_46245 and tr_B4GP34_B4GP34_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29BK5_Q29BK5_DROPS_46245 and tr_B4GP38_B4GP38_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3SUS4_A0A2I3SUS4_PANTR_9598 and tr_A0A2R9CAN2_A0A2R9CAN2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KKV3_A0A2J8KKV3_PANTR_9598 and tr_A0A2R9CE84_A0A2R9CE84_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_G7P7K6_G7P7K6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_A0A0D9RU57_A0A0D9RU57_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_A0A2K5Z4M3_A0A2K5Z4M3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FUS0_F7FUS0_MACMU_9544 and tr_G7NUX0_G7NUX0_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A096NQ85_A0A096NQ85_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A0D9RXW1_A0A0D9RXW1_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K5MG52_A0A2K5MG52_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K6CXC5_A0A2K6CXC5_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K5ZJQ4_A0A2K5ZJQ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZRK3_H0ZRK3_TAEGU_59729 and tr_A0A218VCJ1_A0A218VCJ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7P4E7_G7P4E7_MACFA_9541 and tr_A0A2K6A6Z4_A0A2K6A6Z4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NKX3_A0A096NKX3_PAPAN_9555 and tr_A0A2K5MD24_A0A2K5MD24_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LME4_A0A2I3LME4_PAPAN_9555 and tr_A0A2K5L7V9_A0A2K5L7V9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091J4T0_A0A091J4T0_EGRGA_188379 and tr_A0A091GIU1_A0A091GIU1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091J4T0_A0A091J4T0_EGRGA_188379 and tr_A0A091I207_A0A091I207_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A226N6H8_A0A226N6H8_CALSU_9009 and tr_A0A226P945_A0A226P945_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NME5_A0A226NME5_CALSU_9009 and tr_A0A226PKP6_A0A226PKP6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4AX76_A0A2U4AX76_TURTR_9739 and tr_A0A2Y9Q5C7_A0A2Y9Q5C7_DELLE_9749 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/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.raxml.reduced.phy Alignment comprises 1 partitions and 314 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 314 Gaps: 13.51 % Invariant sites: 0.64 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.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/Q9GZR5/3_mltree/Q9GZR5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 79 / 6320 [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: -145959.121349 [00:00:00 -145959.121349] Initial branch length optimization [00:00:00 -142410.229422] Model parameter optimization (eps = 0.100000) [00:00:22] Tree #1, final logLikelihood: -142152.337367 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.121032,0.182853) (0.289968,0.348296) (0.353789,1.026575) (0.235210,2.183929) 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/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/4_raxmlng_ancestral/Q9GZR5.raxml.log Analysis started: 14-Jul-2021 23:10:12 / finished: 14-Jul-2021 23:10:37 Elapsed time: 25.677 seconds