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 17:30:25 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/2_msa/Q96I59_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/3_mltree/Q96I59.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/4_raxmlng_ancestral/Q96I59 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626100225
  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/Q96I59/2_msa/Q96I59_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 477 sites

WARNING: Sequences tr_J3KK71_J3KK71_COCIM_246410 and tr_A0A0J6Y2H2_A0A0J6Y2H2_COCIT_404692 are exactly identical!
WARNING: Sequences tr_D8RG18_D8RG18_SELML_88036 and tr_D8SPH2_D8SPH2_SELML_88036 are exactly identical!
WARNING: Sequences tr_B8MZN2_B8MZN2_ASPFN_332952 and tr_Q2UQE3_Q2UQE3_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_C6H776_C6H776_AJECH_544712 and tr_F0U6I2_F0U6I2_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0G940_A0A0E0G940_ORYNI_4536 and tr_A2WQ40_A2WQ40_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0G940_A0A0E0G940_ORYNI_4536 and tr_A0A0E0C219_A0A0E0C219_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0G940_A0A0E0G940_ORYNI_4536 and tr_Q93WM3_Q93WM3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G7XDS5_G7XDS5_ASPKW_1033177 and tr_A0A146FEZ3_A0A146FEZ3_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1NN54_I1NN54_ORYGL_4538 and tr_A0A0D3ENW2_A0A0D3ENW2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_G2YP09_G2YP09_BOTF4_999810 and tr_M7TSP9_M7TSP9_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_B3RN59_B3RN59_TRIAD_10228 and tr_A0A369SAP7_A0A369SAP7_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M4CF17_M4CF17_BRARP_51351 and tr_A0A078H4I7_A0A078H4I7_BRANA_3708 are exactly identical!
WARNING: Sequences tr_N4UAL9_N4UAL9_FUSC1_1229664 and tr_X0DER9_X0DER9_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_N4UAL9_N4UAL9_FUSC1_1229664 and tr_A0A2H3TIM7_A0A2H3TIM7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W2QRW3_W2QRW3_PHYPN_761204 and tr_A0A0W8CNF7_A0A0W8CNF7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QRW3_W2QRW3_PHYPN_761204 and tr_W2HJP1_W2HJP1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RDL9_W2RDL9_PHYPN_761204 and tr_A0A0W8DW65_A0A0W8DW65_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A0D3GR15_A0A0D3GR15_9ORYZ_65489 and tr_A0A0E0AJR4_A0A0E0AJR4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A067EL65_A0A067EL65_CITSI_2711 and tr_A0A2H5PDK0_A0A2H5PDK0_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078FII3_A0A078FII3_BRANA_3708 and tr_A0A0D3B343_A0A0D3B343_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078HFK0_A0A078HFK0_BRANA_3708 and tr_A0A0D3A7C9_A0A0D3A7C9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0F8WYG2_A0A0F8WYG2_9EURO_308745 and tr_A0A2T5LME2_A0A2T5LME2_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A1S3XQZ7_A0A1S3XQZ7_TOBAC_4097 and tr_A0A1U7YDS2_A0A1U7YDS2_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YGP6_A0A1S3YGP6_TOBAC_4097 and tr_A0A1U7XZ96_A0A1U7XZ96_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4APD0_A0A1S4APD0_TOBAC_4097 and tr_A0A1U7VGB4_A0A1U7VGB4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2I1EDP4_A0A2I1EDP4_9GLOM_588596 and tr_U9V8N0_U9V8N0_RHIID_747089 are exactly identical!
WARNING: Duplicate sequences found: 26

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/Q96I59/4_raxmlng_ancestral/Q96I59.raxml.reduced.phy

Alignment comprises 1 partitions and 477 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 477
Gaps: 11.23 %
Invariant sites: 0.42 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/4_raxmlng_ancestral/Q96I59.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/Q96I59/3_mltree/Q96I59.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600
[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: -265224.752980

[00:00:00 -265224.752980] Initial branch length optimization
[00:00:01 -265009.208015] Model parameter optimization (eps = 0.100000)

[00:00:31] Tree #1, final logLikelihood: -264571.820501


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.148043,0.318451) (0.333751,0.417192) (0.232835,0.896285) (0.285371,2.119806) 
   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/Q96I59/4_raxmlng_ancestral/Q96I59.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/4_raxmlng_ancestral/Q96I59.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/4_raxmlng_ancestral/Q96I59.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96I59/4_raxmlng_ancestral/Q96I59.raxml.log

Analysis started: 12-Jul-2021 17:30:25 / finished: 12-Jul-2021 17:31:01

Elapsed time: 35.847 seconds

Consumed energy: 3.062 Wh