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 18:11:31 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/2_msa/P10523_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/3_mltree/P10523.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/4_raxmlng_ancestral/P10523 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622646691
  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/P10523/2_msa/P10523_nogap_msa.fasta
[00:00:00] Loaded alignment with 712 taxa and 405 sites

WARNING: Sequences tr_B4Q8D8_B4Q8D8_DROSI_7240 and tr_B4I5E2_B4I5E2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_Q9V393_Q9V393_DROME_7227 and tr_B4IJ49_B4IJ49_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G1S4Y2_G1S4Y2_NOMLE_61853 and tr_G3R2M1_G3R2M1_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1S4Y2_G1S4Y2_NOMLE_61853 and tr_H2R1Z2_H2R1Z2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1S4Y2_G1S4Y2_NOMLE_61853 and sp_P49407_ARRB1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1S4Y2_G1S4Y2_NOMLE_61853 and tr_A0A0D9QVC6_A0A0D9QVC6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1S4Y2_G1S4Y2_NOMLE_61853 and tr_A0A2K5N7Q6_A0A2K5N7Q6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1S6G2_G1S6G2_NOMLE_61853 and sp_Q5RCR4_ARRB2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1S6G2_G1S6G2_NOMLE_61853 and sp_P32121_ARRB2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QRU2_G3QRU2_GORGO_9595 and tr_H2QBY1_H2QBY1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QRU2_G3QRU2_GORGO_9595 and tr_A0A0D9RKX9_A0A0D9RKX9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_Q29D09_Q29D09_DROPS_46245 and tr_B4H9J2_B4H9J2_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29LC9_Q29LC9_DROPS_46245 and tr_B4GQ70_B4GQ70_DROPE_7234 are exactly identical!
WARNING: Sequences tr_W5PNY5_W5PNY5_SHEEP_9940 and sp_P17870_ARRB1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A087ZUT4_A0A087ZUT4_APIME_7460 and tr_A0A2A3EQU3_A0A2A3EQU3_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NG06_A0A158NG06_ATTCE_12957 and tr_A0A195B294_A0A195B294_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4WI29_F4WI29_ACREC_103372 and tr_A0A151WUS5_A0A151WUS5_9HYME_64791 are exactly identical!
WARNING: Sequences tr_F4WI29_F4WI29_ACREC_103372 and tr_A0A151JSD1_A0A151JSD1_9HYME_471704 are exactly identical!
WARNING: Sequences tr_F4WI29_F4WI29_ACREC_103372 and tr_A0A195CVL7_A0A195CVL7_9HYME_456900 are exactly identical!
WARNING: Sequences tr_B3S7M0_B3S7M0_TRIAD_10228 and tr_A0A369SMP9_A0A369SMP9_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G3X811_G3X811_BOVIN_9913 and sp_P32120_ARRB2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A0V0S507_A0A0V0S507_9BILA_6336 and tr_A0A0V0X385_A0A0V0X385_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0S507_A0A0V0S507_9BILA_6336 and tr_A0A0V0VZ11_A0A0V0VZ11_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0S507_A0A0V0S507_9BILA_6336 and tr_A0A0V1LMH6_A0A0V1LMH6_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0S507_A0A0V0S507_9BILA_6336 and tr_A0A0V1H6Q3_A0A0V1H6Q3_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A0V0S507_A0A0V0S507_9BILA_6336 and tr_A0A0V0UB16_A0A0V0UB16_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0SRQ6_A0A2D0SRQ6_ICTPU_7998 and tr_W5U8Q8_W5U8Q8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5NFL3_A0A2K5NFL3_CERAT_9531 and tr_A0A2K6APP7_A0A2K6APP7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K6BLY5_A0A2K6BLY5_MACNE_9545 and tr_A0A2K5ZBV6_A0A2K5ZBV6_MANLE_9568 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/P10523/4_raxmlng_ancestral/P10523.raxml.reduced.phy

Alignment comprises 1 partitions and 405 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 405
Gaps: 15.11 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/4_raxmlng_ancestral/P10523.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/P10523/3_mltree/P10523.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 102 / 8160
[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: -98966.422098

[00:00:00 -98966.422098] Initial branch length optimization
[00:00:00 -98652.110802] Model parameter optimization (eps = 0.100000)

[00:00:23] Tree #1, final logLikelihood: -98099.713261


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.237649,0.444414) (0.181467,0.519126) (0.354282,0.809018) (0.226602,2.266358) 
   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/P10523/4_raxmlng_ancestral/P10523.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/4_raxmlng_ancestral/P10523.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/4_raxmlng_ancestral/P10523.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10523/4_raxmlng_ancestral/P10523.raxml.log

Analysis started: 02-Jun-2021 18:11:31 / finished: 02-Jun-2021 18:11:57

Elapsed time: 25.688 seconds

Consumed energy: 2.128 Wh