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 18-Jun-2021 13:00:13 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/2_msa/P49768_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1624010413
  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_040621/phylogeny-snakemake/results/P49768/2_msa/P49768_nogap_msa.fasta
[00:00:00] Loaded alignment with 629 taxa and 467 sites

WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_H2Q8K1_H2Q8K1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and sp_P49768_PSN1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_F7AGU8_F7AGU8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_G7PAT1_G7PAT1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5N1F1_A0A2K5N1F1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K6CVX6_A0A2K6CVX6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5YUS1_A0A2K5YUS1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2R9BSY5_A0A2R9BSY5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A2J8U215_A0A2J8U215_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and sp_P49810_PSN2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A0D9RUZ9_A0A0D9RUZ9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2R821_H2R821_PANTR_9598 and tr_A0A2R9A5I7_A0A2R9A5I7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0FK13_A0A0E0FK13_ORYNI_4536 and tr_A0A0E0MUL4_A0A0E0MUL4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A096MR14_A0A096MR14_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A2K6CMA8_A0A2K6CMA8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A2K5XVZ1_A0A2K5XVZ1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A015ICJ2_A0A015ICJ2_9GLOM_1432141 and tr_U9UMQ1_U9UMQ1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0D9ZAC7_A0A0D9ZAC7_9ORYZ_40148 and tr_C7J054_C7J054_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A067FHZ3_A0A067FHZ3_CITSI_2711 and tr_A0A2H5QAG8_A0A2H5QAG8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2LVY9_A0A0D2LVY9_GOSRA_29730 and tr_A0A1U8P253_A0A1U8P253_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2PEP2_A0A0D2PEP2_GOSRA_29730 and tr_A0A1U8NMF4_A0A1U8NMF4_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V0UQH5_A0A0V0UQH5_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V1LU29_A0A0V1LU29_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V1NV59_A0A0V1NV59_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V0TJL5_A0A0V0TJL5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3XK05_A0A1S3XK05_TOBAC_4097 and tr_A0A1U7VCP0_A0A1U7VCP0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZTL3_A0A1S3ZTL3_TOBAC_4097 and tr_A0A1U7VRH0_A0A1U7VRH0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2U4A8E9_A0A2U4A8E9_TURTR_9739 and tr_A0A2Y9NSH6_A0A2Y9NSH6_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 28

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.raxml.reduced.phy

Alignment comprises 1 partitions and 467 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 467
Gaps: 22.31 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.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_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 117 / 9360
[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: -142716.050594

[00:00:00 -142716.050594] Initial branch length optimization
[00:00:00 -134365.413762] Model parameter optimization (eps = 0.100000)

[00:00:34] Tree #1, final logLikelihood: -133520.166064


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.232861,0.306914) (0.191490,0.553912) (0.259079,0.587013) (0.316570,2.117637) 
   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_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/4_raxmlng_ancestral/P49768.raxml.log

Analysis started: 18-Jun-2021 13:00:13 / finished: 18-Jun-2021 13:00:49

Elapsed time: 36.698 seconds