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 04-Jun-2021 14:13:43 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/2_msa/P57059_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/3_mltree/P57059.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/4_raxmlng_ancestral/P57059 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805223 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/P57059/2_msa/P57059_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 783 sites WARNING: Sequences tr_A0A2I3HYE2_A0A2I3HYE2_NOMLE_61853 and sp_Q7KZI7_MARK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HYE2_A0A2I3HYE2_NOMLE_61853 and tr_A0A2R9AQR7_A0A2R9AQR7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QF81_G3QF81_GORGO_9595 and tr_H2N3N7_H2N3N7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QF81_G3QF81_GORGO_9595 and tr_A0A2R9B216_A0A2R9B216_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QWR7_G3QWR7_GORGO_9595 and sp_P27448_MARK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RWJ5_G3RWJ5_GORGO_9595 and sp_Q9H0K1_SIK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QL36_H2QL36_PANTR_9598 and tr_A0A2R9AJS8_A0A2R9AJS8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088AHA2_A0A088AHA2_APIME_7460 and tr_A0A2A3E2W7_A0A2A3E2W7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NA53_A0A158NA53_ATTCE_12957 and tr_A0A195DLN5_A0A195DLN5_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NA53_A0A158NA53_ATTCE_12957 and tr_A0A195BJ45_A0A195BJ45_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NA53_A0A158NA53_ATTCE_12957 and tr_A0A195FR84_A0A195FR84_9HYME_34720 are exactly identical! WARNING: Sequences tr_F6TA28_F6TA28_MACMU_9544 and tr_A0A096MPH8_A0A096MPH8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6TA28_F6TA28_MACMU_9544 and tr_A0A2K6EC31_A0A2K6EC31_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZYA3_F6ZYA3_MACMU_9544 and tr_A0A2I3LQ00_A0A2I3LQ00_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H0YWZ5_H0YWZ5_TAEGU_59729 and tr_A0A218UVN9_A0A218UVN9_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4W7Z3_F4W7Z3_ACREC_103372 and tr_A0A195D7T3_A0A195D7T3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A3Q0KCJ0_A0A3Q0KCJ0_SCHMA_6183 and tr_G4LVH5_G4LVH5_SCHMA_6183 are exactly identical! WARNING: Sequences tr_G7NTY3_G7NTY3_MACFA_9541 and tr_A0A2K6B490_A0A2K6B490_MACNE_9545 are exactly identical! WARNING: Sequences tr_U3IDL6_U3IDL6_ANAPL_8839 and tr_A0A091INZ3_A0A091INZ3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IDL6_U3IDL6_ANAPL_8839 and tr_A0A087QXD2_A0A087QXD2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A096MM32_A0A096MM32_PAPAN_9555 and tr_A0A2K6DQ16_A0A2K6DQ16_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MM32_A0A096MM32_PAPAN_9555 and tr_A0A2K5YF23_A0A2K5YF23_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091J0M9_A0A091J0M9_EGRGA_188379 and tr_A0A091WB72_A0A091WB72_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J0M9_A0A091J0M9_EGRGA_188379 and tr_A0A087R5A8_A0A087R5A8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J0M9_A0A091J0M9_EGRGA_188379 and tr_A0A091XH76_A0A091XH76_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091J0M9_A0A091J0M9_EGRGA_188379 and tr_A0A0A0AVX8_A0A0A0AVX8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0X6W5_A0A0V0X6W5_9BILA_92179 and tr_A0A0V1LTQ6_A0A0V1LTQ6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VTX9_A0A0V0VTX9_9BILA_181606 and tr_A0A0V0UGN5_A0A0V0UGN5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1N0R2_A0A0V1N0R2_9BILA_268474 and tr_A0A0V1HVF5_A0A0V1HVF5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3JC30_A0A1S3JC30_LINUN_7574 and tr_A0A1S3JDB4_A0A1S3JDB4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1D1UG16_A0A1D1UG16_RAMVA_947166 and tr_A0A1D1UJL1_A0A1D1UJL1_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2D0STW7_A0A2D0STW7_ICTPU_7998 and tr_A0A2D0SUZ4_A0A2D0SUZ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SYL0_A0A2D0SYL0_ICTPU_7998 and tr_A0A2D0SZ17_A0A2D0SZ17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SYL5_A0A2D0SYL5_ICTPU_7998 and tr_A0A2D0SZK8_A0A2D0SZK8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SYN1_A0A2D0SYN1_ICTPU_7998 and tr_A0A2D0SYN8_A0A2D0SYN8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LT46_A0A2K5LT46_CERAT_9531 and tr_A0A2K6CTD4_A0A2K6CTD4_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 36 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/P57059/4_raxmlng_ancestral/P57059.raxml.reduced.phy Alignment comprises 1 partitions and 783 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 783 Gaps: 29.13 % Invariant sites: 0.38 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/4_raxmlng_ancestral/P57059.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/P57059/3_mltree/P57059.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680 [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: -250103.346284 [00:00:00 -250103.346284] Initial branch length optimization [00:00:01 -214846.081547] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -214450.359404 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.135878,0.136667) (0.110069,0.182384) (0.248210,0.629708) (0.505843,1.591512) 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/P57059/4_raxmlng_ancestral/P57059.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/4_raxmlng_ancestral/P57059.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/4_raxmlng_ancestral/P57059.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P57059/4_raxmlng_ancestral/P57059.raxml.log Analysis started: 04-Jun-2021 14:13:43 / finished: 04-Jun-2021 14:14:31 Elapsed time: 47.774 seconds