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 02-Jun-2021 15:12:45 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/2_msa/P12644_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/3_mltree/P12644.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635965 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_020621/phylogeny-snakemake/results/P12644/2_msa/P12644_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 408 sites WARNING: Sequences sp_P23359_BMP7_MOUSE_10090 and tr_G3V6W8_G3V6W8_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YC83_M3YC83_MUSPF_9669 and tr_A0A2Y9J4Z9_A0A2Y9J4Z9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QSX0_G3QSX0_GORGO_9595 and sp_Q9UK05_GDF2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QSX0_G3QSX0_GORGO_9595 and tr_A0A2R8ZGL7_A0A2R8ZGL7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_H2Q8B9_H2Q8B9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_B0CM38_B0CM38_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A0D9RQR1_A0A0D9RQR1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A2K5NPX8_A0A2K5NPX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A2K6AGA5_A0A2K6AGA5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1NA46_G1NA46_MELGA_9103 and tr_A0A091JLD8_A0A091JLD8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1NA46_G1NA46_MELGA_9103 and tr_A0A093PGL7_A0A093PGL7_9PASS_328815 are exactly identical! WARNING: Sequences sp_P91699_DECA_DROPS_46245 and tr_B4GSL3_B4GSL3_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QKM7_H2QKM7_PANTR_9598 and sp_P18075_BMP7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QKM7_H2QKM7_PANTR_9598 and tr_A0A096NNJ3_A0A096NNJ3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QKM7_H2QKM7_PANTR_9598 and tr_A0A0D9RSE9_A0A0D9RSE9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QKM7_H2QKM7_PANTR_9598 and tr_A0A2K5KKN9_A0A2K5KKN9_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QKM7_H2QKM7_PANTR_9598 and tr_A0A2R9AT21_A0A2R9AT21_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088AQN8_A0A088AQN8_APIME_7460 and tr_A0A2A3EIB7_A0A2A3EIB7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158P1S4_A0A158P1S4_ATTCE_12957 and tr_A0A195BSU4_A0A195BSU4_9HYME_520822 are exactly identical! WARNING: Sequences tr_G0MY06_G0MY06_CAEBE_135651 and tr_G0PL14_G0PL14_CAEBE_135651 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A2I3MVB6_A0A2I3MVB6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A096NKT8_A0A096NKT8_PAPAN_9555 and tr_A0A2K5N9E7_A0A2K5N9E7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NKT8_A0A096NKT8_PAPAN_9555 and tr_A0A2K6CHI7_A0A2K6CHI7_MACNE_9545 are exactly identical! WARNING: Sequences tr_B0CM78_B0CM78_PAPAN_9555 and tr_A0A0D9RDH1_A0A0D9RDH1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_B0CM78_B0CM78_PAPAN_9555 and tr_A0A2K6BCE3_A0A2K6BCE3_MACNE_9545 are exactly identical! WARNING: Sequences tr_B0CM78_B0CM78_PAPAN_9555 and tr_A0A2K5Z7Q6_A0A2K5Z7Q6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151ML35_A0A151ML35_ALLMI_8496 and tr_A0A1U7RB56_A0A1U7RB56_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P086_A0A151P086_ALLMI_8496 and tr_A0A1U7S1W5_A0A1U7S1W5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IZH0_A0A091IZH0_EGRGA_188379 and tr_A0A091VR03_A0A091VR03_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091UPQ9_A0A091UPQ9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A087R890_A0A087R890_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093PIW4_A0A093PIW4_9PASS_328815 and tr_A0A091W333_A0A091W333_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093PIW4_A0A093PIW4_9PASS_328815 and tr_A0A087R1U6_A0A087R1U6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V3E0_A0A091V3E0_NIPNI_128390 and tr_A0A091I9M7_A0A091I9M7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091W8G1_A0A091W8G1_OPIHO_30419 and tr_A0A0A0AKS8_A0A0A0AKS8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W8G1_A0A091W8G1_OPIHO_30419 and tr_A0A091IBT1_A0A091IBT1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0A0AKP2_A0A0A0AKP2_CHAVO_50402 and tr_A0A091HVH4_A0A091HVH4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0WSR4_A0A0V0WSR4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0VIT9_A0A0V0VIT9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V1LAN0_A0A0V1LAN0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V1PEF8_A0A0V1PEF8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0U9I7_A0A0V0U9I7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226MWB1_A0A226MWB1_CALSU_9009 and tr_A0A226PGR7_A0A226PGR7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NDT4_A0A226NDT4_CALSU_9009 and tr_A0A226PL26_A0A226PL26_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3VEP0_A0A2U3VEP0_ODORO_9708 and tr_A0A2U3YTC5_A0A2U3YTC5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3X364_A0A2U3X364_ODORO_9708 and tr_A0A2Y9IPN4_A0A2Y9IPN4_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 46 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.raxml.reduced.phy Alignment comprises 1 partitions and 408 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 408 Gaps: 22.86 % Invariant sites: 0.98 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.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_020621/phylogeny-snakemake/results/P12644/3_mltree/P12644.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 102 / 8160 [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: -139468.023445 [00:00:00 -139468.023445] Initial branch length optimization [00:00:01 -132424.621867] Model parameter optimization (eps = 0.100000) [00:15:37] Tree #1, final logLikelihood: -132167.356654 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.185351,0.215877) (0.137395,0.404502) (0.327980,0.867408) (0.349274,1.774874) 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_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12644/4_raxmlng_ancestral/P12644.raxml.log Analysis started: 02-Jun-2021 15:12:45 / finished: 02-Jun-2021 15:29:24 Elapsed time: 998.271 seconds