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 03-Jun-2021 02:38:35 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/2_msa/Q13950_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/3_mltree/Q13950.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/4_raxmlng_ancestral/Q13950 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677115
  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/Q13950/2_msa/Q13950_nogap_msa.fasta
[00:00:00] Loaded alignment with 613 taxa and 521 sites

WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_H2P328_H2P328_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2I3TUG2_A0A2I3TUG2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2I3LQ88_A0A2I3LQ88_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2K5NDS2_A0A2K5NDS2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2K6E9Y9_A0A2K6E9Y9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2K5XYL6_A0A2K5XYL6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2YIQ6_A0A2I2YIQ6_GORGO_9595 and tr_A0A2R8Z7Z3_A0A2R8Z7Z3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PJ81_H2PJ81_PONAB_9601 and sp_Q13950_RUNX2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PJ81_H2PJ81_PONAB_9601 and tr_F7FY47_F7FY47_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2PJ81_H2PJ81_PONAB_9601 and tr_A0A2K5MQ33_A0A2K5MQ33_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2J8K3P9_A0A2J8K3P9_PANTR_9598 and tr_A0A2R9B517_A0A2R9B517_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NSU0_A0A158NSU0_ATTCE_12957 and tr_A0A195EXD3_A0A195EXD3_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A158NSW0_A0A158NSW0_ATTCE_12957 and tr_A0A151I083_A0A151I083_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A1P6BRM0_A0A1P6BRM0_BRUMA_6279 and tr_A0A0N4TRM8_A0A0N4TRM8_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A096NWX7_A0A096NWX7_PAPAN_9555 and tr_A0A0D9S872_A0A0D9S872_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NWX7_A0A096NWX7_PAPAN_9555 and tr_A0A2K5KWG4_A0A2K5KWG4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NWX7_A0A096NWX7_PAPAN_9555 and tr_A0A2K6D069_A0A2K6D069_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091JDG8_A0A091JDG8_EGRGA_188379 and tr_A0A091X040_A0A091X040_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JDG8_A0A091JDG8_EGRGA_188379 and tr_A0A087R951_A0A087R951_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JDG8_A0A091JDG8_EGRGA_188379 and tr_A0A091X4V5_A0A091X4V5_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JDG8_A0A091JDG8_EGRGA_188379 and tr_A0A0A0AYU0_A0A0A0AYU0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JDG8_A0A091JDG8_EGRGA_188379 and tr_A0A091I4A5_A0A091I4A5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0V0VKM7_A0A0V0VKM7_9BILA_181606 and tr_A0A0V1LGB9_A0A0V1LGB9_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A151X5S5_A0A151X5S5_9HYME_64791 and tr_A0A195DPM1_A0A195DPM1_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A226NN96_A0A226NN96_CALSU_9009 and tr_A0A226NYY3_A0A226NYY3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q5R5_A0A2D0Q5R5_ICTPU_7998 and tr_A0A2D0Q7F8_A0A2D0Q7F8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3ZQ20_A0A2U3ZQ20_ODORO_9708 and tr_A0A2U3Y1M2_A0A2U3Y1M2_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 27

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/Q13950/4_raxmlng_ancestral/Q13950.raxml.reduced.phy

Alignment comprises 1 partitions and 521 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 521
Gaps: 40.92 %
Invariant sites: 0.19 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/4_raxmlng_ancestral/Q13950.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/Q13950/3_mltree/Q13950.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 131 / 10480
[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: -88857.969644

[00:00:00 -88857.969644] Initial branch length optimization
[00:00:00 -87963.925485] Model parameter optimization (eps = 0.100000)

[00:00:44] Tree #1, final logLikelihood: -87531.331256


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.120234,0.357975) (0.112391,0.916687) (0.252421,0.743017) (0.514953,1.294056) 
   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/Q13950/4_raxmlng_ancestral/Q13950.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/4_raxmlng_ancestral/Q13950.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/4_raxmlng_ancestral/Q13950.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13950/4_raxmlng_ancestral/Q13950.raxml.log

Analysis started: 03-Jun-2021 02:38:35 / finished: 03-Jun-2021 02:39:22

Elapsed time: 47.009 seconds

Consumed energy: 4.025 Wh