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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jun-2021 18:04:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/2_msa/Q9GZX5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/3_mltree/Q9GZX5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646240 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/2_msa/Q9GZX5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 532 sites WARNING: Sequences tr_A0A2I3G6J4_A0A2I3G6J4_NOMLE_61853 and tr_A0A2I2YKC9_A0A2I2YKC9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I2Z1I9_A0A2I2Z1I9_GORGO_9595 and sp_P51508_ZNF81_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QNG3_G3QNG3_GORGO_9595 and tr_H2Q781_H2Q781_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QNG3_G3QNG3_GORGO_9595 and tr_A0A2R8Z7P5_A0A2R8Z7P5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PVH4_H2PVH4_PONAB_9601 and sp_Q5R9S5_ZN182_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3TJW6_A0A2I3TJW6_PANTR_9598 and tr_A0A2R9CIJ9_A0A2R9CIJ9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TNU4_A0A2I3TNU4_PANTR_9598 and sp_P17014_ZNF12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TNU4_A0A2I3TNU4_PANTR_9598 and tr_A0A2R9A3E5_A0A2R9A3E5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TWI2_A0A2I3TWI2_PANTR_9598 and tr_A0A2R9C949_A0A2R9C949_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8IMH5_A0A2J8IMH5_PANTR_9598 and tr_A0A2R9A8R9_A0A2R9A8R9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8IU55_A0A2J8IU55_PANTR_9598 and tr_A0A2R8ZW46_A0A2R8ZW46_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JDP3_A0A2J8JDP3_PANTR_9598 and tr_A0A2R8ZR33_A0A2R8ZR33_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JLK3_A0A2J8JLK3_PANTR_9598 and tr_A0A2R9A954_A0A2R9A954_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8QIB0_A0A2J8QIB0_PANTR_9598 and sp_Q5MCW4_ZN569_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PYV9_H2PYV9_PANTR_9598 and sp_P17025_ZN182_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5QTH3_A0A1D5QTH3_MACMU_9544 and tr_A0A096NF04_A0A096NF04_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QTH3_A0A1D5QTH3_MACMU_9544 and tr_A0A2K5NKB0_A0A2K5NKB0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QTH3_A0A1D5QTH3_MACMU_9544 and tr_A0A2K5XWI3_A0A2K5XWI3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5R403_A0A1D5R403_MACMU_9544 and tr_A0A2K6CQR3_A0A2K6CQR3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6RKS7_F6RKS7_MACMU_9544 and tr_G7PJI4_G7PJI4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_G7PJI5_G7PJI5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_A0A2I3LQN8_A0A2I3LQN8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_A0A2K5MJA9_A0A2K5MJA9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_A0A2K6AK43_A0A2K6AK43_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K5N4G8_A0A2K5N4G8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K6D4D0_A0A2K6D4D0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6X482_F6X482_MACMU_9544 and tr_G7PER6_G7PER6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X482_F6X482_MACMU_9544 and tr_A0A2K6C6G6_A0A2K6C6G6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AFT7_F7AFT7_MACMU_9544 and tr_G7Q2L9_G7Q2L9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FTJ3_F7FTJ3_MACMU_9544 and tr_A0A2K6CFR0_A0A2K6CFR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GB84_F7GB84_MACMU_9544 and tr_A0A2K6BN44_A0A2K6BN44_MACNE_9545 are exactly identical! WARNING: Sequences sp_A2VDP4_ZN567_BOVIN_9913 and tr_F1MTT8_F1MTT8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096N2R2_A0A096N2R2_PAPAN_9555 and tr_A0A2K5MKS5_A0A2K5MKS5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N2R2_A0A096N2R2_PAPAN_9555 and tr_A0A2K5YQS2_A0A2K5YQS2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NAW9_A0A096NAW9_PAPAN_9555 and tr_A0A2K5XDI1_A0A2K5XDI1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NS05_A0A096NS05_PAPAN_9555 and tr_A0A2K5N5Y3_A0A2K5N5Y3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NS05_A0A096NS05_PAPAN_9555 and tr_A0A2K5XNG6_A0A2K5XNG6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P472_A0A096P472_PAPAN_9555 and tr_A0A2K5ZDY2_A0A2K5ZDY2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MU96_A0A0A0MU96_PAPAN_9555 and tr_A0A2K5MK99_A0A2K5MK99_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MVY8_A0A0A0MVY8_PAPAN_9555 and tr_A0A2K5M0K3_A0A2K5M0K3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 and tr_A0A2K5XY05_A0A2K5XY05_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 45 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.raxml.reduced.phy Alignment comprises 1 partitions and 532 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 532 Gaps: 23.61 % Invariant sites: 0.38 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/3_mltree/Q9GZX5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 133 / 10640 [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: -168318.255056 [00:00:00 -168318.255056] Initial branch length optimization [00:00:02 -167702.421390] Model parameter optimization (eps = 0.100000) [00:01:02] Tree #1, final logLikelihood: -167376.406762 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115051,0.342813) (0.132585,0.717311) (0.418216,0.801488) (0.334148,1.586898) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX5/4_raxmlng_ancestral/Q9GZX5.raxml.log Analysis started: 02-Jun-2021 18:04:00 / finished: 02-Jun-2021 18:05:08 Elapsed time: 68.336 seconds Consumed energy: 6.234 Wh