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 12-Jul-2021 17:52:59 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/2_msa/Q8WUY3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/3_mltree/Q8WUY3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626101579
  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/300621_run/phylogeny-snakemake/results/Q8WUY3/2_msa/Q8WUY3_nogap_msa.fasta
[00:00:00] Loaded alignment with 973 taxa and 3088 sites

WARNING: Sequences sp_Q5FWK3_RHG01_MOUSE_10090 and tr_G3GYJ1_G3GYJ1_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q5FWK3_RHG01_MOUSE_10090 and tr_D4A6C5_D4A6C5_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q5FWK3_RHG01_MOUSE_10090 and tr_I3MY85_I3MY85_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_M3Y2A7_M3Y2A7_MUSPF_9669 and tr_M3WJ76_M3WJ76_FELCA_9685 are exactly identical!
WARNING: Sequences sp_Q9VTU3_RG68F_DROME_7227 and tr_B4HFJ2_B4HFJ2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B2W1P2_B2W1P2_PYRTR_426418 and tr_A0A2W1GKD5_A0A2W1GKD5_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_H2NDK7_H2NDK7_PONAB_9601 and tr_A0A2K6E3J3_A0A2K6E3J3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2Q3I0_H2Q3I0_PANTR_9598 and sp_Q07960_RHG01_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q3I0_H2Q3I0_PANTR_9598 and tr_G7PQA9_G7PQA9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2Q3I0_H2Q3I0_PANTR_9598 and tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2R2R4_H2R2R4_PANTR_9598 and tr_A0A2R9C6I2_A0A2R9C6I2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6T7J4_F6T7J4_MACMU_9544 and tr_G8F5T6_G8F5T6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6T7J4_F6T7J4_MACMU_9544 and tr_A0A2K5ZS61_A0A2K5ZS61_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6YH87_F6YH87_MACMU_9544 and tr_A0A2K5MYX8_A0A2K5MYX8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6YH87_F6YH87_MACMU_9544 and tr_A0A2K5ZC97_A0A2K5ZC97_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0YRY1_H0YRY1_TAEGU_59729 and tr_A0A091F3P6_A0A091F3P6_CORBR_85066 are exactly identical!
WARNING: Sequences tr_E3LF89_E3LF89_CAERE_31234 and tr_A0A261BMX2_A0A261BMX2_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_M2SSV8_M2SSV8_COCSN_665912 and tr_M2TK23_M2TK23_COCH5_701091 are exactly identical!
WARNING: Sequences tr_M2SSV8_M2SSV8_COCSN_665912 and tr_W6Y9T8_W6Y9T8_COCCA_930089 are exactly identical!
WARNING: Sequences tr_M2SSV8_M2SSV8_COCSN_665912 and tr_W6ZDX4_W6ZDX4_COCMI_930090 are exactly identical!
WARNING: Sequences tr_V2WLZ3_V2WLZ3_MONRO_1381753 and tr_A0A0W0G547_A0A0W0G547_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A0A1N4I6_A0A0A1N4I6_9FUNG_58291 and tr_A0A0A1NKA8_A0A0A1NKA8_9FUNG_58291 are exactly identical!
WARNING: Sequences tr_A0A087RDP7_A0A087RDP7_APTFO_9233 and tr_A0A099ZWW3_A0A099ZWW3_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MPU8_A0A2I0MPU8_COLLI_8932 and tr_A0A1V4KEP5_A0A1V4KEP5_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1DBR9_A0A0V1DBR9_TRIBR_45882 and tr_A0A0V0VJ95_A0A0V0VJ95_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1DBR9_A0A0V1DBR9_TRIBR_45882 and tr_A0A0V1L705_A0A0V1L705_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1DBR9_A0A0V1DBR9_TRIBR_45882 and tr_A0A0V0TZE0_A0A0V0TZE0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A226MMZ1_A0A226MMZ1_CALSU_9009 and tr_A0A226NZT9_A0A226NZT9_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2G4SGJ4_A0A2G4SGJ4_9FUNG_1340429 and tr_A0A367JC03_A0A367JC03_9FUNG_86630 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/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.raxml.reduced.phy

Alignment comprises 1 partitions and 3088 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 3088
Gaps: 85.93 %
Invariant sites: 0.06 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.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/300621_run/phylogeny-snakemake/results/Q8WUY3/3_mltree/Q8WUY3.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 772 / 61760
[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: -602707.392578

[00:00:01 -602707.392578] Initial branch length optimization
[00:00:08 -342682.525999] Model parameter optimization (eps = 0.100000)

[00:04:30] Tree #1, final logLikelihood: -339951.619100


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.125815,0.418823) (0.106377,1.025297) (0.334406,0.600907) (0.433401,1.470440) 
   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/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WUY3/4_raxmlng_ancestral/Q8WUY3.raxml.log

Analysis started: 12-Jul-2021 17:52:59 / finished: 12-Jul-2021 17:57:55

Elapsed time: 296.406 seconds

Consumed energy: 19.452 Wh