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 15:33:10 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/2_msa/Q6KF10_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/3_mltree/Q6KF10.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/4_raxmlng_ancestral/Q6KF10 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622637190 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/Q6KF10/2_msa/Q6KF10_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 455 sites WARNING: Sequences tr_B0XHY0_B0XHY0_CULQU_7176 and tr_B0XHY1_B0XHY1_CULQU_7176 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 sp_O95393_BMP10_HUMAN_9606 and tr_A0A2R9CI72_A0A2R9CI72_PANPA_9597 are exactly identical! WARNING: Sequences sp_P12643_BMP2_HUMAN_9606 and tr_A0A2R9ABN7_A0A2R9ABN7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0K0J809_A0A0K0J809_BRUMA_6279 and tr_A0A0R3QJL8_A0A0R3QJL8_9BILA_42155 are exactly identical! WARNING: Sequences tr_F6TKR2_F6TKR2_MACMU_9544 and tr_A0A096N8T8_A0A096N8T8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6TKR2_F6TKR2_MACMU_9544 and tr_A0A2K5KRR0_A0A2K5KRR0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6TKR2_F6TKR2_MACMU_9544 and tr_A0A2K6DRR8_A0A2K6DRR8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6TKR2_F6TKR2_MACMU_9544 and tr_A0A2K5Y8R7_A0A2K5Y8R7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HMW7_F7HMW7_MACMU_9544 and tr_G7PEU8_G7PEU8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H0Z0M1_H0Z0M1_TAEGU_59729 and tr_A0A218U8P4_A0A218U8P4_9PASE_299123 are exactly identical! WARNING: Sequences tr_G0MY06_G0MY06_CAEBE_135651 and tr_G0PL14_G0PL14_CAEBE_135651 are exactly identical! WARNING: Sequences tr_B3S0I2_B3S0I2_TRIAD_10228 and tr_A0A369SEF4_A0A369SEF4_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A2I3MVB6_A0A2I3MVB6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A0D9RM38_A0A0D9RM38_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A2K6CS17_A0A2K6CS17_MACNE_9545 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_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_A0A091IVU3_A0A091IVU3_EGRGA_188379 and tr_A0A091IE24_A0A091IE24_CALAN_9244 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_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091W8G1_A0A091W8G1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A0A0AKS8_A0A0A0AKS8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091IBT1_A0A091IBT1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093PIW4_A0A093PIW4_9PASS_328815 and tr_A0A091W333_A0A091W333_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0A0AKP2_A0A0A0AKP2_CHAVO_50402 and tr_A0A091HVH4_A0A091HVH4_CALAN_9244 are exactly identical! WARNING: Sequences tr_R7VX22_R7VX22_COLLI_8932 and tr_A0A1V4KR50_A0A1V4KR50_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0SEC4_A0A0V0SEC4_9BILA_6336 and tr_A0A0V1D703_A0A0V1D703_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SEC4_A0A0V0SEC4_9BILA_6336 and tr_A0A0V1LLW5_A0A0V1LLW5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SEC4_A0A0V0SEC4_9BILA_6336 and tr_A0A0V0UFH5_A0A0V0UFH5_9BILA_144512 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_A0A0V0U9I7_A0A0V0U9I7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1AC85_A0A0V1AC85_9BILA_990121 and tr_A0A0V1P764_A0A0V1P764_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A226MNG7_A0A226MNG7_CALSU_9009 and tr_A0A226P2H3_A0A226P2H3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MY82_A0A226MY82_CALSU_9009 and tr_A0A226NPR4_A0A226NPR4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V2A1_A0A2U3V2A1_TURTR_9739 and tr_A0A2Y9MIG4_A0A2Y9MIG4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VEP0_A0A2U3VEP0_ODORO_9708 and tr_A0A2U3YTC5_A0A2U3YTC5_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q6KF10/4_raxmlng_ancestral/Q6KF10.raxml.reduced.phy Alignment comprises 1 partitions and 455 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 455 Gaps: 33.10 % Invariant sites: 0.88 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/4_raxmlng_ancestral/Q6KF10.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/Q6KF10/3_mltree/Q6KF10.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 114 / 9120 [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: -161079.616625 [00:00:00 -161079.616625] Initial branch length optimization [00:00:01 -159957.049582] Model parameter optimization (eps = 0.100000) [00:02:00] Tree #1, final logLikelihood: -159662.608612 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.134222,0.180334) (0.091684,0.360302) (0.293035,0.663937) (0.481059,1.555328) 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/Q6KF10/4_raxmlng_ancestral/Q6KF10.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/4_raxmlng_ancestral/Q6KF10.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/4_raxmlng_ancestral/Q6KF10.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6KF10/4_raxmlng_ancestral/Q6KF10.raxml.log Analysis started: 02-Jun-2021 15:33:10 / finished: 02-Jun-2021 15:35:34 Elapsed time: 143.481 seconds