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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 12-Jul-2021 17:43:27 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/2_msa/Q8NEX9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/3_mltree/Q8NEX9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/4_raxmlng_ancestral/Q8NEX9 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626101007
  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/Q8NEX9/2_msa/Q8NEX9_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 313 sites

WARNING: Sequences tr_A0A2I2Z6Q7_A0A2I2Z6Q7_GORGO_9595 and sp_Q9BPW9_DHRS9_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z6Q7_A0A2I2Z6Q7_GORGO_9595 and tr_A0A2R9CIC8_A0A2R9CIC8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8JNA8_A0A2J8JNA8_PANTR_9598 and tr_A0A2R9AZ51_A0A2R9AZ51_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8Q1W5_A0A2J8Q1W5_PANTR_9598 and tr_A0A2R8ZIC3_A0A2R8ZIC3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q698_H2Q698_PANTR_9598 and tr_A0A2R8Z9Y3_A0A2R8Z9Y3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QBB5_H2QBB5_PANTR_9598 and sp_P80365_DHI2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QBB5_H2QBB5_PANTR_9598 and tr_A0A2R9B7K4_A0A2R9B7K4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7H597_F7H597_MACMU_9544 and tr_A0A2K5MR71_A0A2K5MR71_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7H597_F7H597_MACMU_9544 and tr_A0A2K6C183_A0A2K6C183_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MKG3_G7MKG3_MACMU_9544 and tr_G7NYS2_G7NYS2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7MKG3_G7MKG3_MACMU_9544 and tr_A0A2K6BXM3_A0A2K6BXM3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0ZF85_H0ZF85_TAEGU_59729 and tr_A0A218V873_A0A218V873_9PASE_299123 are exactly identical!
WARNING: Sequences tr_B3RT58_B3RT58_TRIAD_10228 and tr_A0A369SGR8_A0A369SGR8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3RTW4_B3RTW4_TRIAD_10228 and tr_A0A369S1M4_A0A369S1M4_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PIF1_G7PIF1_MACFA_9541 and tr_A0A2K6D2H3_A0A2K6D2H3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PIF1_G7PIF1_MACFA_9541 and tr_A0A2K5Y0T7_A0A2K5Y0T7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7PKR5_G7PKR5_MACFA_9541 and tr_A0A2K6DBF4_A0A2K6DBF4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A044S4N3_A0A044S4N3_ONCVO_6282 and tr_A0A182EII6_A0A182EII6_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D9QY86_A0A0D9QY86_CHLSB_60711 and tr_A0A2K6E9W6_A0A2K6E9W6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0V0WAF0_A0A0V0WAF0_9BILA_92179 and tr_A0A0V1KWE7_A0A0V1KWE7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0VNW6_A0A0V0VNW6_9BILA_181606 and tr_A0A0V0ZEF4_A0A0V0ZEF4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0VNW6_A0A0V0VNW6_9BILA_181606 and tr_A0A0V0UB67_A0A0V0UB67_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A226ND63_A0A226ND63_CALSU_9009 and tr_A0A226PM76_A0A226PM76_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5P1M4_A0A2K5P1M4_CERAT_9531 and tr_A0A2K6AL40_A0A2K6AL40_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3V941_A0A2U3V941_TURTR_9739 and tr_A0A2Y9P1L8_A0A2Y9P1L8_DELLE_9749 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/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.raxml.reduced.phy

Alignment comprises 1 partitions and 313 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 313
Gaps: 7.23 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.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/Q8NEX9/3_mltree/Q8NEX9.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 79 / 6320
[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: -194758.673679

[00:00:00 -194758.673679] Initial branch length optimization
[00:00:00 -194571.772448] Model parameter optimization (eps = 0.100000)

[00:00:13] Tree #1, final logLikelihood: -194542.514313


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.119815,0.128033) (0.242106,0.445697) (0.421845,0.934862) (0.216234,2.230857) 
   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/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEX9/4_raxmlng_ancestral/Q8NEX9.raxml.log

Analysis started: 12-Jul-2021 17:43:27 / finished: 12-Jul-2021 17:43:44

Elapsed time: 16.534 seconds

Consumed energy: 1.139 Wh