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 02:45:31 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/2_msa/P51787_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/3_mltree/P51787.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677531
  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/P51787/2_msa/P51787_nogap_msa.fasta
[00:00:00] Loaded alignment with 970 taxa and 676 sites

WARNING: Sequences sp_Q8K3F6_KCNQ3_MOUSE_10090 and sp_O88944_KCNQ3_RAT_10116 are exactly identical!
WARNING: Sequences tr_A1Z856_A1Z856_DROME_7227 and tr_B4HME1_B4HME1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_G3R701_G3R701_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_A0A2I3S1D1_A0A2I3S1D1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and sp_Q9NR82_KCNQ5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_A0A2R9C3J4_A0A2R9C3J4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QKS4_H2QKS4_PANTR_9598 and sp_O43526_KCNQ2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QKS4_H2QKS4_PANTR_9598 and tr_A0A2K5L1K5_A0A2K5L1K5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7A2Q7_F7A2Q7_ORNAN_9258 and tr_Q1AP78_Q1AP78_PIG_9823 are exactly identical!
WARNING: Sequences tr_F7A2Q7_F7A2Q7_ORNAN_9258 and tr_A0A1S3A4Y5_A0A1S3A4Y5_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_A0A158NUT8_A0A158NUT8_ATTCE_12957 and tr_A0A195BAG0_A0A195BAG0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6Q5P1_F6Q5P1_MACMU_9544 and tr_A0A2I3N4U3_A0A2I3N4U3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6Q5P1_F6Q5P1_MACMU_9544 and tr_A0A2K5L5Z3_A0A2K5L5Z3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6Q5P1_F6Q5P1_MACMU_9544 and tr_A0A2K6DCZ5_A0A2K6DCZ5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2I3MAZ8_A0A2I3MAZ8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2K5NHH6_A0A2K5NHH6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2K6E1G7_A0A2K6E1G7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1K376_G1K376_MACMU_9544 and tr_A0A0D9RP73_A0A0D9RP73_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_U3IS72_U3IS72_ANAPL_8839 and tr_A0A091W3N5_A0A091W3N5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3IS72_U3IS72_ANAPL_8839 and tr_A0A091VCP0_A0A091VCP0_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091VLI6_A0A091VLI6_NIPNI_128390 and tr_A0A091G6X5_A0A091G6X5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091WIM2_A0A091WIM2_OPIHO_30419 and tr_A0A099ZF49_A0A099ZF49_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A0V0ZMT8_A0A0V0ZMT8_9BILA_990121 and tr_A0A0V1NPM6_A0A0V1NPM6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0ZMT8_A0A0V0ZMT8_9BILA_990121 and tr_A0A0V0TNR6_A0A0V0TNR6_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0PXA6_A0A2D0PXA6_ICTPU_7998 and tr_A0A2D0PXB4_A0A2D0PXB4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QMW3_A0A2D0QMW3_ICTPU_7998 and tr_A0A2D0QNH2_A0A2D0QNH2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QN80_A0A2D0QN80_ICTPU_7998 and tr_A0A2D0QNG8_A0A2D0QNG8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QN80_A0A2D0QN80_ICTPU_7998 and tr_A0A2D0QQ42_A0A2D0QQ42_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QN80_A0A2D0QN80_ICTPU_7998 and tr_A0A2D0QQV0_A0A2D0QQV0_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/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787.raxml.reduced.phy

Alignment comprises 1 partitions and 676 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 676
Gaps: 40.34 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787.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/P51787/3_mltree/P51787.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 169 / 13520
[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: -185969.343924

[00:00:00 -185969.343924] Initial branch length optimization
[00:00:02 -173769.164346] Model parameter optimization (eps = 0.100000)

[00:01:32] Tree #1, final logLikelihood: -172629.915405


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.116339,0.335649) (0.103605,0.929446) (0.329507,0.413932) (0.450550,1.616387) 
   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/P51787/4_raxmlng_ancestral/P51787.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51787/4_raxmlng_ancestral/P51787.raxml.log

Analysis started: 03-Jun-2021 02:45:31 / finished: 03-Jun-2021 02:47:10

Elapsed time: 98.904 seconds

Consumed energy: 5.109 Wh