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 02-Jun-2021 18:38:13 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/2_msa/P38571_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/3_mltree/P38571.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/4_raxmlng_ancestral/P38571 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622648293
  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/P38571/2_msa/P38571_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 399 sites

WARNING: Sequences tr_B4Q9R3_B4Q9R3_DROSI_7240 and tr_Q9VKS5_Q9VKS5_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4Q9R3_B4Q9R3_DROSI_7240 and tr_B4HWT2_B4HWT2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G3QN03_G3QN03_GORGO_9595 and tr_H2Q287_H2Q287_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QN03_G3QN03_GORGO_9595 and sp_P38571_LICH_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QN03_G3QN03_GORGO_9595 and tr_A0A2R9BPL4_A0A2R9BPL4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29KR3_Q29KR3_DROPS_46245 and tr_B4GSX7_B4GSX7_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2Q282_H2Q282_PANTR_9598 and tr_A0A2R9A4B8_A0A2R9A4B8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5R0C7_A0A1D5R0C7_MACMU_9544 and tr_G7PDH5_G7PDH5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6YQE6_F6YQE6_MACMU_9544 and tr_G7PDH4_G7PDH4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6YQE6_F6YQE6_MACMU_9544 and tr_A0A2K6CC08_A0A2K6CC08_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7EC56_F7EC56_MACMU_9544 and tr_G7PDI0_G7PDI0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FHQ4_F7FHQ4_MACMU_9544 and tr_G7PDH3_G7PDH3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_W2R7M4_W2R7M4_PHYPN_761204 and tr_A0A0W8C2H3_A0A0W8C2H3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2R7N3_W2R7N3_PHYPN_761204 and tr_A0A0W8C2D5_A0A0W8C2D5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A096P5C6_A0A096P5C6_PAPAN_9555 and tr_A0A0D9R3H6_A0A0D9R3H6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P5D1_A0A096P5D1_PAPAN_9555 and tr_A0A0D9R3A2_A0A0D9R3A2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P5D1_A0A096P5D1_PAPAN_9555 and tr_A0A2K5L2U2_A0A2K5L2U2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P5D1_A0A096P5D1_PAPAN_9555 and tr_A0A2K5ZC39_A0A2K5ZC39_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A078J3P9_A0A078J3P9_BRANA_3708 and tr_A0A0D3EFL0_A0A0D3EFL0_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0V1CVY4_A0A0V1CVY4_TRIBR_45882 and tr_A0A0V0VY06_A0A0V0VY06_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CVY4_A0A0V1CVY4_TRIBR_45882 and tr_A0A0V1PE95_A0A0V1PE95_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CVY4_A0A0V1CVY4_TRIBR_45882 and tr_A0A0V0U8A1_A0A0V0U8A1_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1D9M0_A0A0V1D9M0_TRIBR_45882 and tr_A0A0V1P6X6_A0A0V1P6X6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1N9E9_A0A0V1N9E9_9BILA_268474 and tr_A0A0V1I418_A0A0V1I418_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1I7TD72_A0A1I7TD72_9PELO_1561998 and tr_A0A1I7TD73_A0A1I7TD73_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1U7Q2I6_A0A1U7Q2I6_MESAU_10036 and sp_Q3YBN2_TALLP_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2K5L9U3_A0A2K5L9U3_CERAT_9531 and tr_A0A2K5XEK2_A0A2K5XEK2_MANLE_9568 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/P38571/4_raxmlng_ancestral/P38571.raxml.reduced.phy

Alignment comprises 1 partitions and 399 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 399
Gaps: 6.56 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/4_raxmlng_ancestral/P38571.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/P38571/3_mltree/P38571.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 100 / 8000
[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: -264352.189281

[00:00:00 -264352.189281] Initial branch length optimization
[00:00:01 -263535.368696] Model parameter optimization (eps = 0.100000)

[00:00:28] Tree #1, final logLikelihood: -262684.015525


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.162879,0.322812) (0.230787,0.472975) (0.374049,1.042189) (0.232285,1.930537) 
   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/P38571/4_raxmlng_ancestral/P38571.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/4_raxmlng_ancestral/P38571.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/4_raxmlng_ancestral/P38571.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P38571/4_raxmlng_ancestral/P38571.raxml.log

Analysis started: 02-Jun-2021 18:38:13 / finished: 02-Jun-2021 18:38:45

Elapsed time: 32.534 seconds

Consumed energy: 2.358 Wh