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 12-Jul-2021 17:25:53 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/2_msa/Q5VT97_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/3_mltree/Q5VT97.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099953
  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/300621_run/phylogeny-snakemake/results/Q5VT97/2_msa/Q5VT97_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1194 sites

WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and tr_G3RAD4_G3RAD4_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and tr_H2PMI5_H2PMI5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and tr_H2R2E9_H2R2E9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and sp_P52757_CHIO_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and tr_F7DU99_F7DU99_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3H2B1_A0A2I3H2B1_NOMLE_61853 and tr_A0A2R9AIP2_A0A2R9AIP2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B6QT21_B6QT21_TALMQ_441960 and tr_A0A093XW31_A0A093XW31_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8NUZ1_B8NUZ1_ASPFN_332952 and tr_Q2U511_Q2U511_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NUZ1_B8NUZ1_ASPFN_332952 and tr_A0A1S9DIS5_A0A1S9DIS5_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_F9G5U2_F9G5U2_FUSOF_660025 and tr_N4TH49_N4TH49_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G5U2_F9G5U2_FUSOF_660025 and tr_X0D5Y6_X0D5Y6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9G5U2_F9G5U2_FUSOF_660025 and tr_A0A2H3GQQ3_A0A2H3GQQ3_FUSOX_327505 are exactly identical!
WARNING: Sequences sp_Q8IWW6_RHG12_HUMAN_9606 and tr_A0A2R9A7K9_A0A2R9A7K9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7H6M3_F7H6M3_MACMU_9544 and tr_G7PKJ1_G7PKJ1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7H6M3_F7H6M3_MACMU_9544 and tr_A0A2K5ML85_A0A2K5ML85_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7H6M3_F7H6M3_MACMU_9544 and tr_A0A2K5ZUS6_A0A2K5ZUS6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HHG8_F7HHG8_MACMU_9544 and tr_A0A096P414_A0A096P414_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7XFP6_G7XFP6_ASPKW_1033177 and tr_A0A317UYD0_A0A317UYD0_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_G7PEP6_G7PEP6_MACFA_9541 and tr_A0A2K6AP36_A0A2K6AP36_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PEP6_G7PEP6_MACFA_9541 and tr_A0A2K5ZPJ2_A0A2K5ZPJ2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091JH32_A0A091JH32_EGRGA_188379 and tr_A0A091UU05_A0A091UU05_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A2I0LZ63_A0A2I0LZ63_COLLI_8932 and tr_A0A1V4JRJ9_A0A1V4JRJ9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A100IP11_A0A100IP11_ASPNG_5061 and tr_A0A1L9N2P4_A0A1L9N2P4_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1C3YM95_A0A1C3YM95_GIBZE_229533 and tr_A0A2T4GPA3_A0A2T4GPA3_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A2D0SJI5_A0A2D0SJI5_ICTPU_7998 and tr_A0A2D0SK39_A0A2D0SK39_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.raxml.reduced.phy

Alignment comprises 1 partitions and 1194 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1194
Gaps: 55.75 %
Invariant sites: 0.08 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.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/300621_run/phylogeny-snakemake/results/Q5VT97/3_mltree/Q5VT97.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 299 / 23920
[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: -373105.887226

[00:00:00 -373105.887226] Initial branch length optimization
[00:00:02 -347683.645393] Model parameter optimization (eps = 0.100000)

[00:00:55] Tree #1, final logLikelihood: -346879.391856


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.058631,0.190446) (0.056735,0.233308) (0.298328,0.640478) (0.586307,1.338079) 
   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/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VT97/4_raxmlng_ancestral/Q5VT97.raxml.log

Analysis started: 12-Jul-2021 17:25:53 / finished: 12-Jul-2021 17:26:59

Elapsed time: 65.996 seconds

Consumed energy: 5.022 Wh