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 23-Jun-2021 00:41:09 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/2_msa/P21802_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/3_mltree/P21802.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1624398069
  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/030621_run/phylogeny-snakemake/results/P21802/2_msa/P21802_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 821 sites

WARNING: Sequences tr_F1P3S0_F1P3S0_CHICK_9031 and sp_P18460_FGFR3_CHICK_9031 are exactly identical!
WARNING: Sequences tr_M3YE16_M3YE16_MUSPF_9669 and tr_A0A2Y9J985_A0A2Y9J985_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QZ51_G3QZ51_GORGO_9595 and tr_H2Q2P3_H2Q2P3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QZ51_G3QZ51_GORGO_9595 and tr_A0A2R9B2V2_A0A2R9B2V2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3RMA9_A0A2I3RMA9_PANTR_9598 and sp_P11362_FGFR1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3RMA9_A0A2I3RMA9_PANTR_9598 and tr_G7PD75_G7PD75_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3RMA9_A0A2I3RMA9_PANTR_9598 and tr_A0A096MT31_A0A096MT31_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2Q1T9_H2Q1T9_PANTR_9598 and tr_A0A2R9B0Q5_A0A2R9B0Q5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QPH6_H2QPH6_PANTR_9598 and sp_P35968_VGFR2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QPH6_H2QPH6_PANTR_9598 and tr_A0A2R9CED2_A0A2R9CED2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A2I3LIL7_A0A2I3LIL7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A0D9QXC2_A0A0D9QXC2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A2K5MTR7_A0A2K5MTR7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7E313_F7E313_MACMU_9544 and tr_G7P5T2_G7P5T2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7E313_F7E313_MACMU_9544 and tr_A0A0D9QY88_A0A0D9QY88_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7E313_F7E313_MACMU_9544 and tr_A0A2K6DVH4_A0A2K6DVH4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7E313_F7E313_MACMU_9544 and tr_A0A2K5ZP61_A0A2K5ZP61_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7PE88_G7PE88_MACFA_9541 and tr_A0A2K6DJ09_A0A2K6DJ09_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096N6L3_A0A096N6L3_PAPAN_9555 and tr_A0A2K5XX73_A0A2K5XX73_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P476_A0A096P476_PAPAN_9555 and tr_A0A2K5MKU6_A0A2K5MKU6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P476_A0A096P476_PAPAN_9555 and tr_A0A2K6CCS4_A0A2K6CCS4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I0MF50_A0A2I0MF50_COLLI_8932 and tr_A0A1V4KJL4_A0A1V4KJL4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A226MVT1_A0A226MVT1_CALSU_9009 and tr_A0A226P9Q2_A0A226P9Q2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NJY3_A0A226NJY3_CALSU_9009 and tr_A0A226P8X8_A0A226P8X8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q2J2_A0A2D0Q2J2_ICTPU_7998 and tr_A0A2D0Q3G5_A0A2D0Q3G5_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.raxml.reduced.phy

Alignment comprises 1 partitions and 821 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 821
Gaps: 21.05 %
Invariant sites: 0.24 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.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/030621_run/phylogeny-snakemake/results/P21802/3_mltree/P21802.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 206 / 16480
[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: -245733.301772

[00:00:00 -245733.301772] Initial branch length optimization
[00:00:01 -244512.010486] Model parameter optimization (eps = 0.100000)

[00:00:55] Tree #1, final logLikelihood: -244059.890243


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.162075,0.226561) (0.132454,0.377298) (0.433361,0.874140) (0.272111,1.964229) 
   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/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P21802/4_raxmlng_ancestral/P21802.raxml.log

Analysis started: 23-Jun-2021 00:41:09 / finished: 23-Jun-2021 00:42:13

Elapsed time: 63.654 seconds

Consumed energy: 3.598 Wh