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 17:20:08 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/2_msa/P0C881_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/3_mltree/P0C881.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626099608
  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/P0C881/2_msa/P0C881_nogap_msa.fasta
[00:00:00] Loaded alignment with 999 taxa and 870 sites

WARNING: Sequences tr_A0A0F7VBC6_A0A0F7VBC6_TOXGV_432359 and tr_A0A074STU9_A0A074STU9_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_B6KGM6_B6KGM6_TOXGV_432359 and tr_A0A074T5R8_A0A074T5R8_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_A0A0E0GSF6_A0A0E0GSF6_ORYNI_4536 and tr_A0A0E0P037_A0A0E0P037_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GSI1_A0A0E0GSI1_ORYNI_4536 and tr_B8AQB0_B8AQB0_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0D5D7_A0A0E0D5D7_9ORYZ_40149 and tr_A0A0E0P070_A0A0E0P070_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0D5D7_A0A0E0D5D7_9ORYZ_40149 and tr_A0A0D9ZC73_A0A0D9ZC73_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_B3S2M3_B3S2M3_TRIAD_10228 and tr_A0A369SMW2_A0A369SMW2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M4CVT4_M4CVT4_BRARP_51351 and tr_A0A078JF58_A0A078JF58_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EEA9_M4EEA9_BRARP_51351 and tr_A0A078FEQ6_A0A078FEQ6_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M7ZNL0_M7ZNL0_TRIUA_4572 and tr_A0A3B6I0X0_A0A3B6I0X0_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A078FP56_A0A078FP56_BRANA_3708 and tr_A0A0D3ARB5_A0A0D3ARB5_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_V4S233_V4S233_9ROSI_85681 and tr_A0A2H5Q1T8_A0A2H5Q1T8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4T1A9_V4T1A9_9ROSI_85681 and tr_A0A2H5QQG8_A0A2H5QQG8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2NYI6_A0A0D2NYI6_GOSRA_29730 and tr_A0A1U8NSS3_A0A1U8NSS3_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2UVZ3_A0A0D2UVZ3_GOSRA_29730 and tr_A0A1U8J8X7_A0A1U8J8X7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A1S3X5R0_A0A1S3X5R0_TOBAC_4097 and tr_A0A1U7WB42_A0A1U7WB42_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3Y297_A0A1S3Y297_TOBAC_4097 and tr_A0A1U7Y131_A0A1U7Y131_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YFY6_A0A1S3YFY6_TOBAC_4097 and tr_A0A1U7WUD7_A0A1U7WUD7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3Z237_A0A1S3Z237_TOBAC_4097 and tr_A0A1U7YW74_A0A1U7YW74_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A7F0_A0A1S4A7F0_TOBAC_4097 and tr_A0A1U7YFT1_A0A1U7YFT1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BZ99_A0A1S4BZ99_TOBAC_4097 and tr_A0A1U7WWE4_A0A1U7WWE4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DNX7_A0A1S4DNX7_TOBAC_4097 and tr_A0A1U7XMT0_A0A1U7XMT0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3U3Z0_A0A1S3U3Z0_VIGRR_3916 and tr_A0A3Q0EYW8_A0A3Q0EYW8_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3VKU4_A0A1S3VKU4_VIGRR_3916 and tr_A0A3Q0FFS6_A0A3Q0FFS6_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2U1N1L7_A0A2U1N1L7_ARTAN_35608 and tr_A0A2U1QH66_A0A2U1QH66_ARTAN_35608 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/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881.raxml.reduced.phy

Alignment comprises 1 partitions and 870 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 870
Gaps: 51.78 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881.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/P0C881/3_mltree/P0C881.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 218 / 17440
[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: -358805.007448

[00:00:00 -358805.007448] Initial branch length optimization
[00:00:02 -347130.683357] Model parameter optimization (eps = 0.100000)

[00:01:01] Tree #1, final logLikelihood: -346395.492850


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.043751,0.266948) (0.091609,0.651360) (0.427135,0.704057) (0.437506,1.435234) 
   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/P0C881/4_raxmlng_ancestral/P0C881.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C881/4_raxmlng_ancestral/P0C881.raxml.log

Analysis started: 12-Jul-2021 17:20:08 / finished: 12-Jul-2021 17:21:17

Elapsed time: 69.204 seconds

Consumed energy: 5.648 Wh