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 02:01:47 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/2_msa/Q12866_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/3_mltree/Q12866.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/4_raxmlng_ancestral/Q12866 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622674907
  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/Q12866/2_msa/Q12866_nogap_msa.fasta
[00:00:00] Loaded alignment with 998 taxa and 999 sites

WARNING: Sequences tr_A0A0A0MXS4_A0A0A0MXS4_PONAB_9601 and sp_Q2IBD8_MET_PONAB_9601 are exactly identical!
WARNING: Sequences tr_J9P743_J9P743_CANLF_9615 and sp_Q75ZY9_MET_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2I3S7G9_A0A2I3S7G9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2R9BA11_A0A2R9BA11_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3T1S4_A0A2I3T1S4_PANTR_9598 and tr_A0A2R9BKS2_A0A2R9BKS2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TWE6_A0A2I3TWE6_PANTR_9598 and sp_P42684_ABL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3TWE6_A0A2I3TWE6_PANTR_9598 and tr_F7AU70_F7AU70_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3TWE6_A0A2I3TWE6_PANTR_9598 and tr_A0A2I3MIM0_A0A2I3MIM0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6TG07_F6TG07_HORSE_9796 and tr_L5L0C9_L5L0C9_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_H0WNV1_H0WNV1_OTOGA_30611 and sp_Q2QLH6_MET_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_P08069_IGF1R_HUMAN_9606 and tr_G7P9I7_G7P9I7_MACFA_9541 are exactly identical!
WARNING: Sequences sp_P08069_IGF1R_HUMAN_9606 and tr_A0A2I3MLM3_A0A2I3MLM3_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_P08069_IGF1R_HUMAN_9606 and tr_A0A2K6D2L3_A0A2K6D2L3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5RB36_A0A1D5RB36_MACMU_9544 and tr_A0A2I3M4K4_A0A2I3M4K4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9YUX8_H9YUX8_MACMU_9544 and tr_G7PRB8_G7PRB8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H0ZEE4_H0ZEE4_TAEGU_59729 and tr_A0A218V095_A0A218V095_9PASE_299123 are exactly identical!
WARNING: Sequences sp_Q769I5_MET_BOVIN_9913 and tr_Z4YHD9_Z4YHD9_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A0A0MVB9_A0A0A0MVB9_PAPAN_9555 and tr_A0A2K5LH75_A0A2K5LH75_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0A0MVB9_A0A0A0MVB9_PAPAN_9555 and tr_A0A2K6AMU0_A0A2K6AMU0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091IVQ4_A0A091IVQ4_EGRGA_188379 and tr_A0A091VGU9_A0A091VGU9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IVQ4_A0A091IVQ4_EGRGA_188379 and tr_A0A087R5C7_A0A087R5C7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091IVQ4_A0A091IVQ4_EGRGA_188379 and tr_A0A093K1W3_A0A093K1W3_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 and tr_A0A091URD2_A0A091URD2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A093PK85_A0A093PK85_9PASS_328815 and tr_A0A218V5K2_A0A218V5K2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A3Q0DWU7_A0A3Q0DWU7_TARSY_1868482 and tr_A0A2R9A2B5_A0A2R9A2B5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A3Q0DWU7_A0A3Q0DWU7_TARSY_1868482 and tr_A0A2U3XZR5_A0A2U3XZR5_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2D0RPL8_A0A2D0RPL8_ICTPU_7998 and tr_W5U9F6_W5U9F6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5MLR5_A0A2K5MLR5_CERAT_9531 and tr_A0A2K6D6I9_A0A2K6D6I9_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 28

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/Q12866/4_raxmlng_ancestral/Q12866.raxml.reduced.phy

Alignment comprises 1 partitions and 999 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 999
Gaps: 34.87 %
Invariant sites: 0.40 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/4_raxmlng_ancestral/Q12866.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/Q12866/3_mltree/Q12866.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 250 / 20000
[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: -377609.348081

[00:00:00 -377609.348081] Initial branch length optimization
[00:00:02 -314978.772539] Model parameter optimization (eps = 0.100000)

[00:01:14] Tree #1, final logLikelihood: -314423.466154


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.100488,0.173969) (0.105043,0.251216) (0.370803,0.765984) (0.423666,1.586392) 
   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/Q12866/4_raxmlng_ancestral/Q12866.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/4_raxmlng_ancestral/Q12866.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/4_raxmlng_ancestral/Q12866.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12866/4_raxmlng_ancestral/Q12866.raxml.log

Analysis started: 03-Jun-2021 02:01:47 / finished: 03-Jun-2021 02:03:11

Elapsed time: 83.669 seconds

Consumed energy: 5.784 Wh