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 31-Jul-2021 21:23:53 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/2_msa/Q562E7_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/4_raxmlng_ancestral/Q562E7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627755833 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/Q562E7/2_msa/Q562E7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1941 sites WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2I3S7H5_A0A2I3S7H5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and sp_Q8NFP9_NBEA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_F6YF98_F6YF98_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A287BJF5_A0A287BJF5_PIG_9823 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K5LHX6_A0A2K5LHX6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K6BCF5_A0A2K6BCF5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2Y9ESM2_A0A2Y9ESM2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_E2QWB6_E2QWB6_CANLF_9615 and tr_A0A337S5P0_A0A337S5P0_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and sp_Q8IZQ1_WDFY3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and tr_A0A2R9CBV9_A0A2R9CBV9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_G7P517_G7P517_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K6CVR0_A0A2K6CVR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_I1PFD6_I1PFD6_ORYGL_4538 and tr_A0A0D9ZD04_A0A0D9ZD04_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G7P6E3_G7P6E3_MACFA_9541 and tr_A0A2K5MPI5_A0A2K5MPI5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P6E3_G7P6E3_MACFA_9541 and tr_A0A2K6B0W8_A0A2K6B0W8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7P6E3_G7P6E3_MACFA_9541 and tr_A0A2K5Y3U6_A0A2K5Y3U6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PEU3_G7PEU3_MACFA_9541 and tr_A0A2K6AMA8_A0A2K6AMA8_MACNE_9545 are exactly identical! WARNING: Sequences tr_W2PU23_W2PU23_PHYPN_761204 and tr_A0A0W8C7X3_A0A0W8C7X3_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PY36_W2PY36_PHYPN_761204 and tr_W2KUT5_W2KUT5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015LMU6_A0A015LMU6_9GLOM_1432141 and tr_A0A2H5RZT9_A0A2H5RZT9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096MWM6_A0A096MWM6_PAPAN_9555 and tr_A0A2K5L9D9_A0A2K5L9D9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091JTD1_A0A091JTD1_EGRGA_188379 and tr_A0A087QGX7_A0A087QGX7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JTD1_A0A091JTD1_EGRGA_188379 and tr_A0A091G2K0_A0A091G2K0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UPV5_A0A091UPV5_NIPNI_128390 and tr_A0A087R3Z2_A0A087R3Z2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UPV5_A0A091UPV5_NIPNI_128390 and tr_A0A0A0AXP7_A0A0A0AXP7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CDN0_A0A0V1CDN0_TRIBR_45882 and tr_A0A0V0V6P7_A0A0V0V6P7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 and tr_A0A0V0VEV7_A0A0V0VEV7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 and tr_A0A0V1KYD0_A0A0V1KYD0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A2Y9M8G0_A0A2Y9M8G0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A384AXN8_A0A384AXN8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9KMF9_A0A2Y9KMF9_ENHLU_391180 and tr_A0A384C9Q3_A0A384C9Q3_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 31 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/Q562E7/4_raxmlng_ancestral/Q562E7.raxml.reduced.phy Alignment comprises 1 partitions and 1941 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1941 Gaps: 57.42 % Invariant sites: 0.05 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/4_raxmlng_ancestral/Q562E7.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/Q562E7/3_mltree/Q562E7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 486 / 38880 [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: -529107.834255 [00:00:00 -529107.834255] Initial branch length optimization [00:00:03 -526646.649623] Model parameter optimization (eps = 0.100000) [00:01:55] Tree #1, final logLikelihood: -525048.971958 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.066918,0.333377) (0.134666,0.477822) (0.401895,0.783230) (0.396521,1.509551) 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/Q562E7/4_raxmlng_ancestral/Q562E7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/4_raxmlng_ancestral/Q562E7.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/4_raxmlng_ancestral/Q562E7.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/4_raxmlng_ancestral/Q562E7.raxml.log Analysis started: 31-Jul-2021 21:23:53 / finished: 31-Jul-2021 21:26:05 Elapsed time: 132.123 seconds