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 02:40:31 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/2_msa/P46597_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/3_mltree/P46597.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/4_raxmlng_ancestral/P46597 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677231
  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/P46597/2_msa/P46597_nogap_msa.fasta
[00:00:00] Loaded alignment with 690 taxa and 345 sites

WARNING: Sequences tr_J3KE01_J3KE01_COCIM_246410 and tr_A0A0J7B4M6_A0A0J7B4M6_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QE15_B6QE15_TALMQ_441960 and tr_A0A093UMY9_A0A093UMY9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WJU5_B2WJU5_PYRTR_426418 and tr_A0A2W1CR60_A0A2W1CR60_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G2WV82_G2WV82_VERDV_498257 and tr_A0A0G4LG88_A0A0G4LG88_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_A0A179UU79_A0A179UU79_BLAGS_559298 and tr_C5GSQ4_C5GSQ4_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A0E0I1V5_A0A0E0I1V5_ORYNI_4536 and tr_I1R2T9_I1R2T9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0I1V5_A0A0E0I1V5_ORYNI_4536 and tr_A0A0E0R7B8_A0A0E0R7B8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I1V5_A0A0E0I1V5_ORYNI_4536 and tr_A0A0D3HKW2_A0A0D3HKW2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0J151_A0A0E0J151_ORYNI_4536 and tr_A2ZDP0_A2ZDP0_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A2QYX1_A2QYX1_ASPNC_425011 and tr_A0A319BEE9_A0A319BEE9_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XR34_G7XR34_ASPKW_1033177 and tr_A0A146FTS1_A0A146FTS1_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A251PQM7_A0A251PQM7_PRUPE_3760 and tr_A0A251PQP5_A0A251PQP5_PRUPE_3760 are exactly identical!
WARNING: Sequences tr_I1QYU1_I1QYU1_ORYGL_4538 and tr_A0A0D3HJX7_A0A0D3HJX7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0R7D1_A0A0E0R7D1_ORYRU_4529 and tr_A0A0D3HKX7_A0A0D3HKX7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0R7D1_A0A0E0R7D1_ORYRU_4529 and tr_Q53LW0_Q53LW0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2SRC4_F2SRC4_TRIRC_559305 and tr_A0A178EX93_A0A178EX93_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2T1D4_F2T1D4_TRIRC_559305 and tr_A0A178F9T0_A0A178F9T0_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_V2Y0B3_V2Y0B3_MONRO_1381753 and tr_A0A0W0F518_A0A0W0F518_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A3B6PS90_A0A3B6PS90_WHEAT_4565 and tr_A0A3B6PUY6_A0A3B6PUY6_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A0F8X9N2_A0A0F8X9N2_9EURO_308745 and tr_A0A2T5LW02_A0A2T5LW02_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S3ZH56_A0A1S3ZH56_TOBAC_4097 and tr_A0A1U7VCK4_A0A1U7VCK4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2G3A0K8_A0A2G3A0K8_CAPAN_4072 and tr_A0A2G3CXQ0_A0A2G3CXQ0_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2N5RZ32_A0A2N5RZ32_9BASI_200324 and tr_A0A2N5UIQ3_A0A2N5UIQ3_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 23

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/P46597/4_raxmlng_ancestral/P46597.raxml.reduced.phy

Alignment comprises 1 partitions and 345 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 345
Gaps: 16.15 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/4_raxmlng_ancestral/P46597.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/P46597/3_mltree/P46597.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 87 / 6960
[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: -175905.827760

[00:00:00 -175905.827760] Initial branch length optimization
[00:00:00 -175102.007649] Model parameter optimization (eps = 0.100000)

[00:00:21] Tree #1, final logLikelihood: -174470.910912


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.097392,0.530312) (0.182082,0.481447) (0.385572,0.857930) (0.334954,1.581993) 
   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/P46597/4_raxmlng_ancestral/P46597.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/4_raxmlng_ancestral/P46597.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/4_raxmlng_ancestral/P46597.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P46597/4_raxmlng_ancestral/P46597.raxml.log

Analysis started: 03-Jun-2021 02:40:31 / finished: 03-Jun-2021 02:40:55

Elapsed time: 23.757 seconds

Consumed energy: 1.670 Wh