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 18:23:18 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/2_msa/P58107_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/3_mltree/P58107.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/4_raxmlng_ancestral/P58107 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626103398
  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/P58107/2_msa/P58107_nogap_msa.fasta
[00:00:00] Loaded alignment with 469 taxa and 5088 sites

WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A2K5MBL2_A0A2K5MBL2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A2K6DEV1_A0A2K6DEV1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1B8XZD2_A0A1B8XZD2_XENTR_8364 and tr_F7ESM6_F7ESM6_XENTR_8364 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PT23_A0A2D0PT23_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PT29_A0A2D0PT29_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUI9_A0A2D0PUI9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUJ2_A0A2D0PUJ2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUJ7_A0A2D0PUJ7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUK2_A0A2D0PUK2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUM4_A0A2D0PUM4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWA1_A0A2D0PWA1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWA6_A0A2D0PWA6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWB1_A0A2D0PWB1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PX51_A0A2D0PX51_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPP3_A0A2D0RPP3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPT8_A0A2D0RPT8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPT9_A0A2D0RPT9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPW9_A0A2D0RPW9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQ29_A0A2D0RQ29_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQ32_A0A2D0RQ32_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQN1_A0A2D0RQN1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQP1_A0A2D0RQP1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQW3_A0A2D0RQW3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQX2_A0A2D0RQX2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRC2_A0A2D0RRC2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRF7_A0A2D0RRF7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRG7_A0A2D0RRG7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRK2_A0A2D0RRK2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRL2_A0A2D0RRL2_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 29

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/P58107/4_raxmlng_ancestral/P58107.raxml.reduced.phy

Alignment comprises 1 partitions and 5088 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 5088
Gaps: 74.65 %
Invariant sites: 22.19 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/4_raxmlng_ancestral/P58107.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/P58107/3_mltree/P58107.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 1272 / 101760
[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: -302237.549420

[00:00:00 -302237.549420] Initial branch length optimization
[00:00:05 -300062.822668] Model parameter optimization (eps = 0.100000)

[00:02:59] Tree #1, final logLikelihood: -298396.491960


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.202121,0.531042) (0.124166,0.622580) (0.368977,0.845053) (0.304736,1.652437) 
   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/P58107/4_raxmlng_ancestral/P58107.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/4_raxmlng_ancestral/P58107.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/4_raxmlng_ancestral/P58107.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P58107/4_raxmlng_ancestral/P58107.raxml.log

Analysis started: 12-Jul-2021 18:23:18 / finished: 12-Jul-2021 18:26:40

Elapsed time: 202.185 seconds

Consumed energy: 17.038 Wh