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 03-Jun-2021 02:15:12 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/2_msa/P00492_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/3_mltree/P00492.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/4_raxmlng_ancestral/P00492 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622675712
  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/P00492/2_msa/P00492_nogap_msa.fasta
[00:00:00] Loaded alignment with 517 taxa and 218 sites

WARNING: Sequences tr_G1QNB1_G1QNB1_NOMLE_61853 and tr_G3SIK2_G3SIK2_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QNB1_G1QNB1_NOMLE_61853 and tr_H2PWT8_H2PWT8_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QNB1_G1QNB1_NOMLE_61853 and tr_K7C582_K7C582_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QNB1_G1QNB1_NOMLE_61853 and sp_P00492_HPRT_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QNB1_G1QNB1_NOMLE_61853 and tr_A0A2K5LQT6_A0A2K5LQT6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2N9Z9_H2N9Z9_PONAB_9601 and sp_Q9NRG1_PRDC1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2N9Z9_H2N9Z9_PONAB_9601 and tr_A0A2R9BHH5_A0A2R9BHH5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0F7UZL1_A0A0F7UZL1_TOXGV_432359 and tr_A0A074SSE9_A0A074SSE9_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_F6YAY4_F6YAY4_MACMU_9544 and tr_A0A096P3S0_A0A096P3S0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6YAY4_F6YAY4_MACMU_9544 and tr_A0A0D9RIB3_A0A0D9RIB3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F4P9V2_F4P9V2_BATDJ_684364 and tr_A0A177WVH8_A0A177WVH8_BATDE_403673 are exactly identical!
WARNING: Sequences sp_Q45FY6_HPRT_PIG_9823 and tr_A0A2Y9LSD3_A0A2Y9LSD3_DELLE_9749 are exactly identical!
WARNING: Sequences sp_Q45FY6_HPRT_PIG_9823 and tr_A0A2Y9T5A5_A0A2Y9T5A5_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_E3N1P5_E3N1P5_CAERE_31234 and tr_A0A261C0E5_A0A261C0E5_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8XWA1_A8XWA1_CAEBR_6238 and tr_A0A2G5VSQ6_A0A2G5VSQ6_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_D2H3W9_D2H3W9_AILME_9646 and tr_A0A384CQA4_A0A384CQA4_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3N777_A0A2I3N777_PAPAN_9555 and tr_A0A2K6CGL4_A0A2K6CGL4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3N777_A0A2I3N777_PAPAN_9555 and tr_A0A2K5Y0G0_A0A2K5Y0G0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0A1NQK9_A0A0A1NQK9_9FUNG_58291 and tr_A0A367K3J2_A0A367K3J2_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A091IN54_A0A091IN54_EGRGA_188379 and tr_A0A093QCH0_A0A093QCH0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091IN54_A0A091IN54_EGRGA_188379 and tr_A0A091V1H0_A0A091V1H0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IN54_A0A091IN54_EGRGA_188379 and tr_A0A091G7R5_A0A091G7R5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091IXW7_A0A091IXW7_EGRGA_188379 and tr_A0A091VG20_A0A091VG20_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IXW7_A0A091IXW7_EGRGA_188379 and tr_A0A087QU90_A0A087QU90_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A0V1CHC5_A0A0V1CHC5_TRIBR_45882 and tr_A0A0V1LUL6_A0A0V1LUL6_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CHC5_A0A0V1CHC5_TRIBR_45882 and tr_A0A0V0TMV9_A0A0V0TMV9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3Q918_A0A1S3Q918_SALSA_8030 and tr_A0A060YHH8_A0A060YHH8_ONCMY_8022 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/P00492/4_raxmlng_ancestral/P00492.raxml.reduced.phy

Alignment comprises 1 partitions and 218 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 218
Gaps: 11.77 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/4_raxmlng_ancestral/P00492.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/P00492/3_mltree/P00492.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 55 / 4400
[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: -57666.723509

[00:00:00 -57666.723509] Initial branch length optimization
[00:00:00 -56399.590490] Model parameter optimization (eps = 0.100000)

[00:00:19] Tree #1, final logLikelihood: -56263.197913


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.130117,0.291225) (0.245807,0.394811) (0.381799,0.905233) (0.242277,2.144003) 
   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/P00492/4_raxmlng_ancestral/P00492.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/4_raxmlng_ancestral/P00492.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/4_raxmlng_ancestral/P00492.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00492/4_raxmlng_ancestral/P00492.raxml.log

Analysis started: 03-Jun-2021 02:15:12 / finished: 03-Jun-2021 02:15:33

Elapsed time: 21.132 seconds

Consumed energy: 1.583 Wh