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 17:52:21 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/2_msa/Q16288_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/3_mltree/Q16288.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/4_raxmlng_ancestral/Q16288 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622645541
  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/Q16288/2_msa/Q16288_nogap_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 839 sites

WARNING: Sequences tr_B4Q8R8_B4Q8R8_DROSI_7240 and sp_Q24488_ROR1_DROME_7227 are exactly identical!
WARNING: Sequences tr_A0A2I2Z1Z2_A0A2I2Z1Z2_GORGO_9595 and sp_O15146_MUSK_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2J8MRU2_A0A2J8MRU2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and sp_Q16620_NTRK2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2R9BIL6_A0A2R9BIL6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q292H0_Q292H0_DROPS_46245 and tr_B4GDJ7_B4GDJ7_DROPE_7234 are exactly identical!
WARNING: Sequences tr_E2RKA1_E2RKA1_CANLF_9615 and tr_G1LBG1_G1LBG1_AILME_9646 are exactly identical!
WARNING: Sequences tr_A0A2I3RY88_A0A2I3RY88_PANTR_9598 and tr_A0A2R8ZRG9_A0A2R8ZRG9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TDE7_A0A2I3TDE7_PANTR_9598 and tr_A0A2R8ZYT3_A0A2R8ZYT3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q0H8_H2Q0H8_PANTR_9598 and sp_Q16832_DDR2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q0H8_H2Q0H8_PANTR_9598 and tr_A0A2R9ADM8_A0A2R9ADM8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7FCZ2_F7FCZ2_MONDO_13616 and tr_G3WY32_G3WY32_SARHA_9305 are exactly identical!
WARNING: Sequences sp_Q01973_ROR1_HUMAN_9606 and tr_A0A2R8ZB26_A0A2R8ZB26_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5Q156_A0A1D5Q156_MACMU_9544 and tr_A0A096MUC1_A0A096MUC1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5Q156_A0A1D5Q156_MACMU_9544 and tr_A0A0D9S361_A0A0D9S361_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5RHZ9_A0A1D5RHZ9_MACMU_9544 and tr_A0A2K5LTN5_A0A2K5LTN5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5RHZ9_A0A1D5RHZ9_MACMU_9544 and tr_A0A2K6CF21_A0A2K6CF21_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6RUP2_F6RUP2_MACMU_9544 and tr_A0A2K6ASI9_A0A2K6ASI9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7BW77_F7BW77_MACMU_9544 and tr_A0A0D9R7H0_A0A0D9R7H0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2I3MH64_A0A2I3MH64_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2K6BIB6_A0A2K6BIB6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HFZ8_F7HFZ8_MACMU_9544 and tr_A0A096P0W8_A0A096P0W8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7P9D5_G7P9D5_MACFA_9541 and tr_A0A2K5Y8E4_A0A2K5Y8E4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3LHJ8_A0A2I3LHJ8_PAPAN_9555 and tr_A0A2K5LUK5_A0A2K5LUK5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091J1T1_A0A091J1T1_EGRGA_188379 and tr_A0A087RHY4_A0A087RHY4_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091J1T1_A0A091J1T1_EGRGA_188379 and tr_A0A091H7N1_A0A091H7N1_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A087RHD0_A0A087RHD0_APTFO_9233 and tr_A0A091H1K2_A0A091H1K2_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A0V1CN21_A0A0V1CN21_TRIBR_45882 and tr_A0A0V0UA62_A0A0V0UA62_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0X2J3_A0A0V0X2J3_9BILA_92179 and tr_A0A0V1L3W9_A0A0V1L3W9_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A226NHF2_A0A226NHF2_CALSU_9009 and tr_A0A226PQ01_A0A226PQ01_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0RYH1_A0A2D0RYH1_ICTPU_7998 and tr_W5UGS1_W5UGS1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5L1F0_A0A2K5L1F0_CERAT_9531 and tr_A0A2K6AMP9_A0A2K6AMP9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2U4A3Z7_A0A2U4A3Z7_TURTR_9739 and tr_A0A2Y9NSC8_A0A2Y9NSC8_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 33

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/Q16288/4_raxmlng_ancestral/Q16288.raxml.reduced.phy

Alignment comprises 1 partitions and 839 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 839
Gaps: 32.99 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/4_raxmlng_ancestral/Q16288.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/Q16288/3_mltree/Q16288.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 210 / 16800
[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: -231872.664312

[00:00:00 -231872.664312] Initial branch length optimization
[00:00:01 -226919.376950] Model parameter optimization (eps = 0.100000)

[00:00:49] Tree #1, final logLikelihood: -226342.750136


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.143401,0.267263) (0.123386,0.362054) (0.404064,0.852100) (0.329149,1.739937) 
   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/Q16288/4_raxmlng_ancestral/Q16288.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/4_raxmlng_ancestral/Q16288.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/4_raxmlng_ancestral/Q16288.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16288/4_raxmlng_ancestral/Q16288.raxml.log

Analysis started: 02-Jun-2021 17:52:21 / finished: 02-Jun-2021 17:53:17

Elapsed time: 56.643 seconds

Consumed energy: 3.641 Wh